Lung cancer diagnostics and therapeutics with mir-660

ABSTRACT

Provided are methods of treating lung cancer in a patient in need thereof. The method includes administration to the patient a composition comprising a therapeutically effective amount of a compound that reduces the expression level of E3 ubiquitin-protein ligase MDM2. The compound in certain instances is a miR-660 miRNA, or a functional variant thereof. The patient in need of treatment in certain instances expresses miR-660 in a lung tissue sample or biological fluid sample at a level lower as compared to a control level derived from a subject or plurality of subjects that do not have lung cancer, or as compared to a control level derived from a lung cancer patient or plurality thereof, that have been given a favorable prognosis; expresses MDM2 at a higher level in a lung tissue sample or biological fluid sample as compared to a control level derived from a subject or plurality of subjects that do not have lung cancer, or as compared to a control level derived from a lung cancer patient or plurality thereof that have been given a favorable prognosis; and/or expresses p53 in a lung tissue sample or a biological fluid sample below a control level derived from a lung tumor tissue sample, or plurality thereof, or a biological fluid sample, or plurality thereof, obtained from a patient that has a favorable lung cancer prognosis; or a control level derived from a healthy subject.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation of U.S. patent application Ser. No.16/169,436, filed on Oct. 24, 2018, which is a Continuation of U.S.patent application Ser. No. 14/885,536 filed on Oct. 16, 2015, whichclaims priority to and benefit of provisional application U.S. Ser. No.62/065,217 filed on Oct. 17, 2014, the contents of which areincorporated herein by reference in their entirety.

STATEMENT REGARDING SEQUENCE LISTING

The Sequence Listing associated with this application is provided intext format in lieu of a paper copy, and is hereby incorporated byreference into the specification. The name of the text file containingthe Sequence Listing is GENS-009-C02US-SeqList.txt. The text file is1.84 KB, was created on Dec. 2, 2020, and is being submittedelectronically via EFS-Web.

FIELD OF THE INVENTION

The present invention generally relates to lung cancer diagnostics andtherapeutics. More specifically, the present invention relates tomethods for treating lung cancer and methods for selecting patients whocan benefit from the treatment methods described herein. In someembodiments, the invention is directed to the use of miR-660 indiagnostics, prognostics and treatment of lung cancer.

BACKGROUND OF THE INVENTION

Lung cancer is the leading cause of cancer death worldwide, resulting inmore than 1.4 million deaths per year (Jemal et al. (2011). CA Cancer JClin 61, pp. 69-90). Non-molecular lung cancer diagnostics rely onradiological findings and histological analysis of biopsy tissue. Chestradiography (x-ray) can be used as a screening tool, albeit its lowsensitivity and specificity. Computed tomography (CT) is much moresensitive for detecting small nodules in the lungs that are likely torepresent earlier stages of lung cancer. CT screening trials have shownthat chest radiographs miss 60% to 80% of the lung cancers detected byCT, but CT is more costly and delivers higher amounts of radiation tothe patient. There is also a greater risk of over diagnosis, not only ofnonmalignant lung nodules, but other incidental findings as well.

Lung cancer staging is determined using several criteria. The vastmajority of lung cancers are carcinomas, i.e., malignancies that arisefrom epithelial cells. Based on histological criteria, there are twomain types of lung carcinoma, categorized by the size and appearance ofthe malignant cells: non-small cell (about 85% of lung cancers) andsmall-cell lung carcinoma (about 15%). The non-small cell lungcarcinomas (NSCLC) are grouped together because their prognosis andmanagement are similar. There are three main sub-types: squamous celllung carcinoma (25%), adenocarcinoma (60%), and large cell lungcarcinoma (5%).

Non-small cell lung carcinoma is staged from IA (“one A”; early stage,typically associated with more favorable prognosis) to IV (“four”;advanced stage, typically associated with poor prognosis). Overall, lungcancer is staged based on the extent and size of the tumor (T), lymphnodes (N) involved, and presence of metastases (M).

Often, tumors are discovered as locally advanced or as metastaticdisease, and despite improvements in molecular diagnosis and targetedtherapies, the overall 5-year survival rate remains in the 10-20% range.Indeed, non-small cell lung cancer (NSCLC) is poorly chemosensitive tomost of the available agents with response rates ranging from 10% to 25%(Ettinger et al. (2012). J. Natl Compr Canc Netw 8, pp. 740-801). Thediscovery of recurrent mutations in the epidermal growth factor receptor(EGFR) kinase (Lynch et al. (2004). N Engl J Med 350, pp. 2129-2139), aswell as gene fusion products involving the anaplastic lymphoma kinase(ALK) (Soda et al., (2007). Nature 448, pp. 561-566), has led to amarked change in the treatment of patients with lung adenocarcinoma, themost common type of lung cancer (Youlden et al. (2008). J Thorac Oncol3, pp. 819-831; Jackman and Johnson (2005). Lancet 366, pp. 1385-1396).To date, approximately 10% of lung cancers display mutations in the EGFRgene, the target for EGFR tyrosine kinase inhibitors (TKIs), while onlyabout 5% of tumors have ALK rearrangements that can be targeted by ALKinhibitors (Herbst et al. (2008). N Engl J Med 359, pp. 1367-1380).Thus, the majority of lung tumors lack effective treatment and noveltherapeutic strategies are still needed.

MicroRNAs (miRNAs) are short non-coding RNAs, 20-24 nucleotides long,that play important roles in almost all biological pathways (Bartel(2004). Cell, 116, pp. 281-297; Bartel (2009). Cell 136, pp. 215-233;Lewis et al. (2005). Cell 120, pp. 15-20; Lagos-Quintana et al. (2001)Science 294, pp. 853-858) and influence numerous cancer-relevantprocesses such as proliferation (Xiao et al. (2008) Nat Immunol 9, pp.405-414), cell cycle (He et al., (2007). Nature 447, pp. 1130-1134),apoptosis (Cimmino et al., (2005) Proc Natl Acad Sci USA 102, pp.13944-13949) and migration (Ma et al. (2007) Nature 449, pp. 682-688).MiRNAs are aberrantly expressed in different cancers (Iorio et al.,2005; Calin et al., 2005; Iorio and Croce, 2012; U.S. Patent Publication2011/0251098) and contribute to carcinogenesis by promoting theexpression of oncogenes or by inhibiting the expression of tumorsuppressor genes (Croce, 2009). Many studies have demonstrated thecritical role of miRNAs in lung cancer pathogenesis and their potentialas biomarkers for lung cancer risk stratification (Raponi et al. (2009).Cancer Res 69, pp. 5776-5783), outcome prediction (Yanaihara et al.(2006). Cancer Cell 9, pp. 189-198) and classification of histologicalsubtypes (Takamizawa et al. (2004). Cancer Res 64, pp. 3753-3756; Bishopet al. (2010). Clin Cancer Res 16, pp. 610-619). MiRNAs released bycells can also be found in biological fluids such as plasma, serum, andurine (U.S. Pat. No. 8,486,626) making them suitable as biomarkers inlung cancers such as NSCLC (Boeri et al. (2011) Proc Natl Acad Sci USA108, pp. 3713-3718; Sozzi et al. (2014) J Clin Oncol 32, pp. 768-773;U.S. Pat. No. 8,735,074; U.S. Patent Application Publication2012/0329060).

MiR-660 has been reported to be up-regulated in chronic lymphocyticleukemia (Zhu et al. (2012) Carciogenesis 33, pp. 1294-1301; Ferrer etal. (2013) Leuk Lymphoma 54, pp. 2016-2022) and also in leukemic cellsafter treatment with 4-hydroxynonenal, a compound that inducesdifferentiation and blocks proliferation of leukemic cells (Pizzimentiet al. (2009). Free Radic Biol Med 46, pp. 282-288). Furthermore,miR-660 up-regulation was observed during in vitro differentiation ofmyoblast (Dmitriev et al., 2013a) and facioscapulohumeral musculardystrophy (Dmitriev et al., 2013b). MiR-660 is also involved in theexpansion and production of platelets during megakaryopoiesis (Emmrichet al., 2012). MiR-660 was shown to be deregulated in plasma samples ofNSCLC patients identified in a low-dose computed tomography (LDCT)screening trial (Boeri et al., 2011). Despite some evidence of miR-660de-regulation in cancer, little is known about its role in lungtumorigenesis and its putative target genes.

The p53 tumor suppressor protein is a key regulator of cell cycle G0/G1checkpoint, senescence and apoptosis in response to cellular stresssignals (Levine (1997). Cell 88, pp. 323-331; Wu and Levine (1997). MolMed 3, pp. 441-451). Mouse double minute 2 (MDM2), a p53 E3 ubiquitinligase (Honda et al. (1997). FEBS Lett 420, pp. 25-27), is the principalnegative regulator of the level and function of p53 (Montes de Oca Lunaet al. (1995). Nature 378, pp. 203-206; Chen et al. (1996). Mol CellBiol 16, pp. 2445-2452). MDM2 regulates p53 by various mechanisms(Kubbutat et al. (1997). Nature 387, pp. 299-303; Moll and Petrenko(2003). Mol Cancer Res 1, pp. 1001-1008), e.g., by bindingtransactivation region of p53 (Kussie et al. (1996). Science 274, pp.948-953; Momaid et al. (1992). Cell 69, pp. 1237-1245), promotingnuclear export and cytoplasmic accumulation of p53 by monoubiquitination(Haupt et al. (1997) Nature 387, pp. 296-299; Lai et al. (2001). J BiolChem 276, pp. 31357-31367) and inducing p53 proteosomal degradation bypolyubiquitination (Feng et al. (2004). J Biol Chem 279, pp.35510-35517). In addition, the MDM2 gene is amplified or overexpressedin a variety of human cancers, such as sarcoma (Oliner et al. (1992).Nature 358, pp. 80-83), lymphoma (Capoulade et al. (1998) Oncogene 16,pp. 1603-1610), breast cancer (Marchetti et al. (1995). J Pathol 175,pp. 31-38, lung cancer (Marchetti et al. (1995). Diagn Mol Pathol 4, pp.93-97) and testicular germ cell tumor (Riou et al. (1995). Mol Carcinog12, pp. 124-131), and expression of p53 in lung tumor samples iscorrelated with a positive prognosis (Xu et al., 2013). Additionally,NSCLC patients that have an MDM2 variant that is associated with p53overexpression have better prognosis than patients with an MDM2 variantthat is associated with less p53 overexpression (Han et al., 2008).Several miRNAs target MDM2, including the miR-143/miR-145 cluster whichcan be induced by p53 (Zhang et al. (2013). Oncogene 32, pp. 61-69) aswell as miR-25 and miR-32, which inhibit tumor glioblastoma growth inmouse brain (Suh et al. (2014). Proc Natl Acad Sci USA 109, pp.5316-5321).

SUMMARY OF THE INVENTION

In one aspect, the present invention relates to a pharmaceuticalcomposition comprising a compound that reduces the expression level ofE3 ubiquitin-protein ligase MDM2. The expression level in oneembodiment, is protein expression. In another embodiment, the MDM2expression is mRNA expression. In one embodiment, the pharmaceuticalcomposition comprises an RNA interference (RNAi) compound that targetsMDM2 mRNA expression, for example, a small interfering RNA (siRNA),short hairpin RNA (shRNA) or a micro RNA (miRNA). In a furtherembodiment, the pharmaceutical composition comprises a miR-660oligonucleotide (e.g., a miRNA of SEQ ID NO:2 or 3, or a functionalvariant thereof).

In some embodiments of the pharmaceutical composition comprising acompound that reduces the expression level of E3 ubiquitin-proteinligase MDM2 further comprises a pharmaceutically acceptable carrier.

As provided above, in one embodiment described herein, a pharmaceuticalcomposition comprising an RNAi compound that targets MDM2 mRNAexpression is provided. In one embodiment, the compound is a miR, e.g.,miR-660 (SEQ ID NO: 2, 3) or a miR-660 pre-miR (SEQ ID NO: 1), or afunctional variant thereof. In one embodiment, the miR is at least 90%identical to SEQ ID NO: 2 or SEQ ID NO: 3. In one embodiment, thecompound is a miR-660 functional variant and comprises one or moremodified nucleotides. For example, the compound in one embodiment is amiR-660 functional variant comprising at least one, at least two or atleast three nucleotides and is stable in the patient for a longer periodof time than the compound of SEQ ID NO:2 or SEQ ID NO: 3. In oneembodiment, the compound is encoded by a vector (e.g., a viral vectorsuch as an adeno-associated virus (AAV) vector, or a plasmid basedexpression vector).

In yet another embodiment, the compound that reduces MDM2 mRNAexpression is an RNA compound that comprises the sequence ACCCAUU (SEQID NO: 4) or ACCCATT (SEQ ID NO: 5). In a further embodiment, thecompound comprising the sequence SEQ ID NO: 4 or SEQ ID NO: 5 is ansiRNA, a shRNA, a miRNA or an antisense inhibitor.

In one embodiment, the compound that reduces MDM2 mRNA expression isencoded by a vector. In a further embodiment, the vector encodes asequence selected from SEQ ID NO: 1, 2, 3, or 4, or a variant thereof.

In another aspect, the present invention relates to a method of treatingcancer for example, lung cancer. In one embodiment, the method comprisesadministering to a patient in need thereof, a composition comprising aneffective amount of one of the compounds that reduces MDM2 expression.In a further embodiment, the cancer is lung cancer. The lung cancer is asmall cell lung cancer or a non-small cell lung cancer (NSCLC). Thecompound, as described in embodiments herein, is an RNAi compound thattargets MDM2 expression, e.g., a miR-660 miRNA or a variant thereof. Inone embodiment, the patient in need of treatment (i) expresses miR-660in a lung tissue sample or biological fluid sample at a level lower thana control level derived from a subject or plurality of subjects that donot have lung cancer, or as compared to a control level derived from alung cancer patient or plurality thereof, that have been given afavorable prognosis; (ii) expresses MDM2 at a higher level in a lungtissue sample or biological fluid sample as compared to a control levelderived from a subject or plurality of subjects that do not have lungcancer, or as compared to a control level derived from a lung cancerpatient or plurality thereof that have been given a favorable prognosis;and/or (iii) expresses p53 in a lung tissue sample or a biological fluidsample below a control level derived from a lung tumor tissue sample (orplurality thereof) or a biological fluid sample (or plurality thereof)obtained from a patient that has a favorable lung cancer prognosis; or acontrol level derived from a healthy subject.

In yet another aspect of the invention, a patient in need of treatmentis selected for treatment via a miRNA blood test. For example, apatient's blood sample is interrogated for the expression of at leastfive, at least 10, at least 15, at least 20 or 24 of the miRNAs setforth in Table A. Based on ratios of expression ratios of miRNA pairs, apatient is either selected or not selected for therapy with one of thecompositions described herein. For example, if the ratio of the miRNApair exceeds a cut-off value determined from a comparison to a controlsample or a plurality thereof, the ratio is assigned a positive score.In one embodiment, if at least nine of the miRNA expression ratios areassigned a positive score, the patient is selected for therapy. Inanother embodiment. In one embodiment, the miRNA pairs comprise106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p, 133a/142-3p,140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21, 142-3p/221,142-3p/30b, and 320/660, or the inverse ratios thereof. In a furtherembodiment, the miRNA pairs comprise 106a/660, 106a/92a, 126/660,140-5p/197, 140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p, 17/660,17/92a, 197/660, 197/92a, 19b/660, or 28-3p/660, or the inverse ratiosthereof.

In yet another embodiment, the miRNA pairs comprise 106a/660, 106a/92a,126/660, 140-5p/197, 140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p,17/660, 17/92a, 197/660, 197/92a, 19b/660, and 28-3p/660, or the inverseratios thereof.

TABLE A hsa-miR-16 hsa-miR-320 hsa-miR-148a hsa-miR-17 hsa-miR-451hsa-miR-15b hsa-miR-21 hsa-miR-660 hsa-miR-19b hsa-miR-101 hsa-miR-106ahsa-miR-28-3p hsa-miR-126 hsa-miR-133a hsa-miR-30b hsa -miR-145hsa-miR-140-3p hsa-miR-30c hsa-miR-197 hsa-miR-140-5p hsa-miR-486-5p hsa-miR-221 hsa-miR-142-3p hsa-miR-92a

In some embodiments, a patient in need of treatment with thecompositions and methods provided herein has a lung tumor tissue sampleor a biological fluid sample that expresses p53. In a furtherembodiment, p53 is expressed below a level of p53 expression in a lungtumor tissue sample or a biological fluid sample obtained from a patientthat has a favorable lung cancer prognosis.

In one embodiment, a sample (e.g., biological fluid sample such as ablood sample) from the patient expresses miR-660 (i) below a miR-660level in a noncancerous lung tissue sample from the patient, (ii) belowa miR-660 level in a subject that does not have lung cancer (e.g., ahealthy subject) or (iii) below a mean miR-660 level in a plurality ofsubjects that do not have lung cancer.

In one embodiment, a miR-660 level in a plasma sample from the patientin need of treatment is below a miR-660 level in a plasma sample from asubject that does not have lung cancer (e.g., a healthy subject) or theaverage miR-660 plasma level in a plurality of subjects that do not havelung cancer.

In some embodiments, a lung tumor tissue sample from the patient in needof treatment expresses MDM2 (e.g., MDM2 protein or mRNA). In someembodiments, the MDM2 expression level in the lung tumor tissue isgreater than an MDM2 level in a noncancerous lung tissue sample from thepatient in need of treatment or greater than an MDM2 level in a subjectthat does not have lung cancer (e.g., a healthy subject).

In some embodiments, the patient in need of treatment is selected fortreatment by one of the methods disclosed in U.S. Patent ApplicationPublication No. US 2015/0191794 published Jul. 9, 2015), the contents ofwhich are incorporated by reference herein in their entireties for allpurposes.

Another aspect of the invention relates to a method of evaluating theprognosis of a lung cancer patient. The method comprises measuring theconcentration of miR-660 in a tissue sample or bodily fluid of thepatient, wherein a miR-660 concentration in the patient below a miR-660concentration in the same fluid or tissue of a plurality of lung cancerpatients that had a favorable prognosis indicates that the patient has apoor prognosis.

In yet another aspect, another method of diagnosing lung cancer in apatient is provided. The method comprises measuring the concentration ofmir-660 in (a) tissue suspected of being lung cancer in the patient and(b) normal tissue of the patient, wherein a lower level of miR-660 inthe suspected tissue than in the normal tissue indicates that thesuspected tissue is lung cancer.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1C are graphs showing miR-660 efficient expression manipulationin human lung cancer lines. The graphs on the left show the relativeexpression of miR-660 after transient transfection with miR-660 mimic orcontrol at 24 h, 48 h, 72 h or 96 h; the graphs on the right show therelative expression of mir-660 after stable transfection with mir-660 orcontrol lentiviral vector at 10 d and 30 d. These determinations weremade in three different cell lines: H460 (FIG. 1A), A549 (FIG. 1B) andH1299 (FIG. 1C). All data are expressed as mean standard error of themean (SEM). (n=3, *p<0.05 vs. miRNA mimic control (“mim-ctr”)).

FIGS. 2A-2B are graphs showing that miR-660 is down-regulated in tumortissue and plasma. FIG. 2A is a dot plot showing miR-660 levels inplasma samples. Data were normalized on the average of each card.*p<0.05 vs each group. FIG. 2B is a histogram showing miR-660 expressionlevels in lung cancers compared to normal tissues. Data are expressed asmean±standard error of the mean (SEM). *p<0.05 vs. normal tissues.

FIGS. 3A-3D are images and graphs showing antitumoral effects of miR-660(SEQ ID NO: 2). FIG. 3A shows that miR-660 decreases migratory capacityof lung cancer cells in a Transwell® assay (n=5), and FIG. 3B shows thatmiR-660 decreases invasive capacity of lung cancer cells in aTranswell®assay (n=5). Representative images of migrated/invaded cellsfor each condition are shown. Migration and invasion data are expressedas the number of migrated mir-660 over-expressing cells vs. the numberof migrated control cells. All data are expressed as mean±standard errorof the mean (SEM). *p<0.05 vs. cells transfected with control. FIG. 3Cshows the proliferation of cells transfected with miR-660 or control.Viable cells were counted with trypan blue at 24, 72 and 120 hours tomeasure cell growth. Graphs show the proliferation reduction of miR-660over-expressing cells compared to control cells (n=5). FIG. 3D showsapoptosis, measured as annexin V^(pos)/PI^(neg) cells and expressed as afold increase compared to cell transfected with mimic control (n=5). Alldata are expressed as mean±SEM. *p<0.05 vs. cells transfected withcontrol.

FIGS. 4A-4B are graphs showing that mir-660 over-expression reduces lungcancer cell growth. FIG. 4A shows cells that were transfected withmir-660 or control and viable cells were counted with trypan blue at 72and 120 hours to measure cell growth. Graphs show cell proliferation ofmir-660 over-expressing cells compared to control cells (n=5). FIG. 4Bshows apoptosis measured by flow cytometry as annexin V^(pos)/PI^(neg)cells (left panel) and graphs show the number of apoptotic cellscompared to cell transfected with mimic control (right panel) (n=5). Alldata are expressed as mean±SEM. *p<0.05 vs. cells transfected withcontrol.

FIGS. 5A-5B are a graphic representation and a graph showing that MDM2is a direct target of miR-660. FIG. 5A shows a predicted MDM23′UTR-binding site for miR-660. The figure shows alignment of a miR-660sequence (SEQ ID NO: 2) with a portion of the wild type MDM2 3′UTR (SEQID NO: 7) and mutated MDM2 (SEQ ID NO: 8). FIG. 5B is a bar graphshowing average luciferase activity. Reporter systems were transfectedin HEK293 with wild type MDM2, mutated MDM2, or EMPTY 3′UTR, incombination with miR-660 mimics or control. All data are expressed asmean±SEM. (n=5; *p<0.05).

FIGS. 6A-6B are graphs and photographs of western blots showing thatMDM2 expression is down-modulated after miR-660 over-expression. FIG. 6Ais a graph showing MDM2 mRNA levels in lung cancer cells transfectedwith mimic miR-660 or mimic control (n=5). FIG. 6B shows results of MDM2analysis by western blot (n=4) and representative western blot bands.All data are expressed as mean±SEM. (*p<0.05).

FIGS. 7A-7C are graphs and photographs showing that mir-660 increasedp53 levels and function. FIG. 7A shows p53 levels after mir-660over-expression measured by ELISA (n=4). FIG. 7B shows p21 mRNA levelsin lung cancer cells transfected with mimic mir-660 or mimic control(n=4). FIG. 7C shows p21 expression analysis by western blot (n=4) andrepresentative western blot bands for all cell lines. All data areexpressed as mean±SEM. (*p<0.05).

FIGS. 8A-8F are graphs and photographs showing that stable mir-660expression reduced p53 wt cancer cell functionality. FIG. 8A shows thatstable mir-660 over-expression decreases migratory capacity of lungcancer cells in a Transwell® assay (n=3). FIG. 8B shows that stablemir-660 over-expression decreases invasive capacity of lung cancer cellsin Transwell® assay (n=3). FIG. 8C shows viable cells that were countedwith trypan blue at 72 and 120 hours to measure cell growth. Graphs showthe proliferation reduction of mir-660 over-expressing cells compared tocontrol cells (n=3). FIG. 8D shows apoptosis measured by flow cytometryas annexin V^(pos)/PI^(neg) cells and expressed as number of apoptoticcells compared to control (n=3). FIG. 8E shows representative graphs ofcell cycle analysis in stable mir-660 over-expressing cells compared tocontrols. FIG. 8F shows the results of MDM2 analysis by western blot(n=3) and representative western blot bands. All data are expressed asmean±SEM. *p<0.05 vs. mir-660 cells with control.

FIGS. 9A-9C are graphs and photographs showing that mir-660 inhibitedxenograft tumor growth in mice. Graphs show tumor growth of mir-660over-expressing cells subcutaneously (s.c.) injected in both flanks ofnude mice compared to control (n=5 per group). MiRNAs were stabletransfected in (FIG. 9A) NCI-H460, (FIG. 9B) A549 and (FIG. 9C) H1299.All data are expressed as mean±SEM. (*p<0.05 vs. mim-ctr).Representative images of tumor size for each condition (right panels).

FIGS. 10A-10C are graphs showing inhibition of xenograft tumor growth inmice with miR-660. Graphs show tumor growth of miR-660 over-expressingcells s.c injected in both flanks of nude mice compared to control (n=5per group). MiRNAs were transiently (left panels) or stably transfected(right panels) in (FIG. 10A) NCI-H460, (FIG. 10B) A549 and (FIG. 10C)H1299 cells. All data are expressed as mean±SEM. (*P<0.05 vs mim-ctr).

FIGS. 11A-11D are graphs showing transient mir-660 over-expression delaytumor growth in mice. Graphs show tumor growth of mir-660over-expressing cells s.c. injected in both flanks of nude mice comparedto control (n=5 per group). MiRNAs were transiently transfected in (FIG.11A) NCI-H460, (FIG. 111B) A549, and (FIG. 11C) H1299. (FIG. 11D)Relative expression of mir-660 after transient transfection with mir-660mimic or control in mice tumors. All data are expressed as mean±SEM.(*p<0.05 vs. mim-ctr).

DETAILED DESCRIPTION OF THE INVENTION

Unless defined otherwise all technical and scientific terms used hereinhave the same meaning as commonly understood to one of ordinary skill inthe art to which this disclosure belongs.

As used herein, the singular forms “a” “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. Additionally, the use of “or” is intended to include“and/or”, unless the context clearly indicates otherwise.

As used herein, a “gene” is a polynucleotide that encodes a discreteproduct, whether RNA or proteinaceous in nature. It is appreciated thatmore than one polynucleotide may be capable of encoding a discreteproduct. The term includes alleles and polymorphisms of a gene thatencodes the same product, or a functionally associated (including gain,loss, or modulation of function) analog thereof, based upon chromosomallocation and ability to recombine during normal mitosis.

A “sequence” or “gene sequence” as used herein is a nucleic acidmolecule or polynucleotide composed of a discrete order of nucleotidebases. The term includes the ordering of bases that encodes a discreteproduct (i.e., “coding region”), whether RNA or proteinaceous in nature.It is appreciated that more than one polynucleotide may be capable ofencoding a discrete product. It is also appreciated that alleles andpolymorphisms of the human gene sequences may exist and may be used inthe practice of the disclosure to identify the expression level(s) ofthe gene sequences or an allele or polymorphism thereof. Identificationof an allele or polymorphism depends in part upon chromosomal locationand ability to recombine during mitosis.

An “expressed sequence” is a sequence that is transcribed by cellularprocesses within a cell. To detect an expressed sequence, a region ofthe sequence that is unique relative to other expressed sequences may beused. An expressed sequence may encode a polypeptide product or not beknown to encode any product. So an expressed sequence may contain openreading frames or no open reading frames. Non-limiting examples includeregions of about 8 or more, about 10 or more, about 12 or more, about 14or more, about 16 or more, about 18 or more, about 20 or more, about 22or more, about 24 or more, about 26 or more, about 28 or more, or about30 or more contiguous nucleotides within an expressed sequence may beused. The term “about” as used in the previous sentence refers to anincrease or decrease of 1 from the stated numerical value. The physicalform of an expressed sequence may be an RNA molecule or thecorresponding cDNA molecule.

The terms “correlate” or “correlation” or equivalents thereof refer toan association between expression of one or more genes and anotherevent, such as, but not limited to, physiological phenotype orcharacteristic, such as tumor type.

A “polynucleotide” is a polymeric form of nucleotides of any length,either ribonucleotides or deoxyribonucleotides. This term refers only tothe primary structure of the molecule. Thus, this term includes double-and single-stranded DNA and RNA. It also includes known types ofmodifications including labels known in the art, methylation, “caps”,substitution of one or more of the naturally occurring nucleotides withan analog, and internucleotide modifications such as uncharged linkages(e.g., phosphorothioates, phosphorodithioates, etc.), as well asunmodified forms of the polynucleotide.

The term “amplify” is used in the broad sense to mean creating anamplification product can be made enzymatically with DNA or RNApolymerases. “Amplification” as used herein, generally refers to theprocess of producing multiple copies of a desired sequence, particularlythose of a sample. “Multiple copies” mean at least 2 copies. A “copy”does not necessarily mean perfect sequence complementarity or identityto the template sequence. Methods for amplifying mRNA are generallyknown in the art, and include reverse transcription PCR (RT-PCR) andquantitative PCR (or Q-PCR) or real time PCR. Alternatively, RNA may bedirectly labeled as the corresponding cDNA by methods known in the art.

By “corresponding”, it is meant that a nucleic acid molecule shares asubstantial amount of sequence identity with another nucleic acidmolecule. Substantial amount means at least 95%, usually at least 98%and more usually at least 99%, and sequence identity is determined usingthe BLAST algorithm, as described in Altschul et al. (1990), J. Mol.Biol. 215, pp. 403-410, incorporated by reference herein in itsentirety, e.g., by using the published default setting, i.e., parametersw=4, t=17.

The terms “label” or “labeled” refer to a composition, compound ormoiety capable of producing a detectable signal indicative of thepresence of the labeled molecule. Suitable labels include radioisotopes,nucleotide chromophores, enzymes, substrates, fluorescent molecules,chemiluminescent moieties, magnetic particles, bioluminescent moieties,and the like. As such, a label is any composition detectable byspectroscopic, photochemical, biochemical, immunochemical, electrical,optical, or chemical means.

The term “support” refers to conventional supports such as beads,particles, dipsticks, fibers, filters, membranes and silane or silicatesupports such as glass slides.

“Expression” and “gene expression” include transcription and/ortranslation of nucleic acid material. Expression levels of an expressedsequence may optionally be normalized by reference or comparison to theexpression level(s) of one or more control expressed genes. These“normalization genes” have expression levels that are relativelyconstant in all members of the plurality or group of known tumor types.

As used herein, the term “comprising” and its cognates are used in theirinclusive sense; that is, equivalent to the term “including” and itscorresponding cognates.

Conditions that “allow” an event to occur or conditions that are“suitable” for an event to occur, such as hybridization, strandextension, and the like, or “suitable” conditions are conditions that donot prevent such events from occurring. Thus, these conditions permit,enhance, facilitate, and/or are conducive to the event. Such conditions,known in the art and described herein, depend upon, for example, thenature of the nucleotide sequence, temperature, and buffer conditions.These conditions also depend on what event is desired, such ashybridization, cleavage, strand extension or transcription.

Sequence “mutation,” as used herein, refers to any sequence alterationin the sequence of a gene disclosed herein interest in comparison to areference sequence. A sequence mutation includes single nucleotidechanges, or alterations of more than one nucleotide in a sequence, dueto mechanisms such as substitution, deletion, or insertion. Singlenucleotide polymorphism (SNP) is also a sequence mutation as usedherein. Because embodiments of the present invention are based in parton the relative level of gene expression, mutations in non-codingregions of genes as disclosed herein may also be assayed in the practiceof the disclosure.

“Detection” or “detecting” includes any means of detecting, includingdirect and indirect determination of the level of gene expression andchanges therein.

As used herein, the term “treat” is meant to describe a process by whicha sign or symptom of a disorder is reduced in severity or eliminated.Alternatively, or in addition, a disorder which can occur in multiplelocations, is treated if that disorder is eliminated within at least oneof multiple locations.

Effective dosages are expected to decrease the severity of a sign orsymptom. For instance, a sign or symptom of a disorder, which can occurin multiple locations, is alleviated if the severity of the disorder isdecreased within at least one of multiple locations.

As used herein, the term “severity” is meant to describe an unfavorableprognosis for a subject, a progression of a disorder to a moredeleterious stage, a presentation of a sign or symptom or a diagnosis ofan additional or secondary disorder, a requirement for invasive,experimental, or high-risk medical treatment, an indication that thedisorder has become systemic rather than local or that the disorder hasinvaded additional or secondary bodily systems, the potential of adisorder to transform from a benign to malignant state, or the potentialof a disorder to escalate from a state that is managed by preventative,daily, or routine medicine to a crises state that is managed byemergency medicine or specialize care centers.

As used herein, the term “severity” is also meant to describe thepotential of cancer to transform from a precancerous, or benign, stateinto a malignant state. Alternatively, or in addition, severity is meantto describe, for instance, a cancer stage or grade. In additionalaspects of the invention, severity describes the number and location ofsecondary cancers as well as the operability or drug-accessibility ofthose tumors. In these situations, prolonging the life expectancy of thesubject and/or reducing pain, decreasing the proportion of cancerouscells or restricting cells to one system, and improving cancerstage/tumor grade/histological grade/nuclear grade are consideredalleviating a sign or symptom of the cancer.

As used herein the term “symptom” is defined as an indication ofdisease, illness, or injury in the body. Symptoms are felt or noticed bythe individual experiencing the symptom, but may not easily be noticedby others. Others are defined as non-health-care professionals.

As used herein the term “sign” is also defined as an indication ofdisease, illness, or injury in the body. Signs are defined as thingsthat can be seen by a doctor, nurse, or other health care professional.

“miR-660” as used herein is any miRNA that is derived from the pre-miRNAhaving the stem-loop sequence5′-CUGCUCCUUCUCCCAUACCCAUUGCAUAUCGGAGUUGUGAAUUCUCAAAACACCUCCUGUGUGCAUGGAUUACAGGAGGGUGAGCCUUGUCAUCGUG-3′ (SEQ ID NO: 1), or afunctional variant thereof. For example, in one embodiment, “mir-660”refers to miR-660-5p, having the ribonucleotide sequence5′-uacccauugcauaucggaguug-3′ (SEQ ID NO: 2). In another embodiment, the“mir-660” refers to miR-660-3p, having the ribonucleotide sequence5′-accuccugugugcauggauua-3′ (SEQ ID NO: 3). In certain embodiments ofthe invention, at least one of the miR-660s is substituted with amodified nucleotide which does not substantially affect base pairing ofmiR-660 with other nucleic acids. SEQ ID NOs: 2 and 3 are shownunderlined in the re-miRNA below.

(SEQ ID NO: 1) 5′-CUGCUCCUUC UCCCAUACCC AUUGCAUAUC GGAGUUGUGAAUUCUCAAAA CACCUCCUGU GUGCAUGGAU UACAGGAGGG UGAGCCUUGU CAUCGUG-3′.In some embodiments, the pre-miRNA of SEQ ID NO: 1 is processed into theunderlined sequences by the RNase III enzyme Dicer in the cytoplasm. Insome diagnostic or therapeutic embodiments, particularly where a Diceris present, hsa-miR-660-5p or has-miR-660-3p (or functional variantsthereof) can substitute for miR-660, since hsa-miR 660 is thetherapeutic compound. The term “miR-660” also encompasses functionalvariants of wide-type miR-660, miR-660 mimics or functional variantsthereof.

Thus, the term “microRNA mimic” refers to synthetic non-coding RNAs(i.e., the miRNA is not obtained by purification from a source of theendogenous miRNA) that are capable of entering the RNAi pathway andregulating gene expression. In some embodiments, the miR-660 mimic ishsa-miR-660-5p (SEQ ID NO: 2).

As used herein, the term “functional variant” of miR-660, refers to anucleic acid that is at least 75% (e.g., at least 80%, at least 85%, atleast 90%, at least 95%) identical in sequence to miR-660 and is capableof having one or more biological activities of miR-660. In oneembodiment, the functional variant of miR-660 reduces the expressionlevel of MDM2 mRNA. In some embodiments, a functional variant includes anon-natural nucleic acid, or a plurality thereof.

As used herein, the term “therapeutically effective amount” means theamount of a compound that, when administered to a patient for treating astate, disorder or condition, is sufficient to effect such treatment.The “therapeutically effective amount” will vary depending on thecompound, the disease and its severity and the age, weight, physicalcondition and responsiveness of the mammal to be treated.

The present invention is based in part on the discovery that miR-660interacts with MDM2 to reduce the MDM2-p53 interaction. The manyapplications of this newly discovered interaction include the diagnosisof lung cancer and other cancers, the prognosis of lung cancer and othercancers, and the treatment of lung cancer and other cancers.

In one aspect of the invention, the present invention provides a methodof treating a cancer patient in need thereof, for example a lung cancerpatient, and pharmaceutical compositions useful therefor. In one aspect,the therapeutic method comprises administering to the patient in needthereof a composition comprising a therapeutically effective amount of acompound that reduces the expression level of E3 ubiquitin-proteinligase MDM2, or reduces the interaction of MDM2 with p53 (e.g., an MDM2antibody or fragment thereof). In some embodiments, the compound reducesthe expression level of the MDM2 protein, MDM2 mRNA or a combinationthereof. In one embodiment, the patient in need of treatment (i)expresses miR-660 in a lung tissue sample or biological fluid sample ata level lower than a control level derived from a subject or pluralityof subjects that do not have lung cancer, or as compared to a controllevel derived from a lung cancer patient or plurality thereof, that havebeen given a favorable prognosis; (ii) expresses MDM2 at a higher levelin a lung tissue sample or biological fluid sample as compared to acontrol level derived from a subject or plurality of subjects that donot have lung cancer, or as compared to a control level derived from alung cancer patient or plurality thereof that have been given afavorable prognosis; and/or (iii) expresses p53 in a lung tissue sampleor a biological fluid sample below a control level derived from a lungtumor tissue sample (or plurality thereof) or a biological fluid sample(or plurality thereof) obtained from a patient that has a favorable lungcancer prognosis; or a control level derived from a healthy subject.

In some embodiments, the compound that reduces the expression level ofE3 ubiquitin-protein ligase MDM2 is a nucleic acid. In some embodiments,the compound is an RNA interfering agent, e.g., an siRNA molecule, anshRNA molecule or a miRNA, which reduces the expression level of MDM2.In yet another embodiment, the compound that reduces the interaction ofMDM2 with p53 is an antibody that binds MDM2, or a fragment thereof.

As used herein, the term “RNA interfering agent” is intended toencompass those forms of gene silencing mediated by double-stranded RNA,regardless of whether the RNA interfering agent comprises an siRNA,miRNA, shRNA or other double-stranded RNA molecule.

“Short interfering RNA” (siRNA), also referred to herein as “smallinterfering RNA” is defined as an RNA agent which functions to inhibitexpression of a target gene, e.g., by RNAi. An siRNA may be chemicallysynthesized, produced by in vitro transcription, or produced within ahost cell. In one embodiment, siRNA is a double stranded RNA (dsRNA)molecule of about 15 to about 40 nucleotides in length, for exampleabout 15 to about 28 nucleotides, about 19 to about 25 nucleotides inlength, or about 19, about 20, about 21, about 22, or about 23nucleotides in length, and may contain a 3′ and/or 5′ overhang on eachstrand having a length of about 0, 1, 2, 3, 4, or 5 nucleotides. Thelength of the overhang is independent between the two strands, i.e., thelength of the overhang on one strand is not dependent on the length ofthe overhang on the second strand. In some embodiments, the siRNA iscapable of promoting RNA interference through degradation or specificpost-transcriptional gene silencing (PTGS) of the target messenger RNA(mRNA).

siRNAs also include small hairpin (also called stem loop) RNAs (shRNAs).In one embodiment, these shRNAs are composed of a short (e.g., about 19to about 25 nucleotide) antisense strand, followed by a nucleotide loopof about 5 to about 9 nucleotides, and the analogous sense strand.Alternatively, the sense strand may precede the nucleotide loopstructure and the antisense strand may follow. These shRNAs may becontained in plasmids, retroviruses, and lentiviruses and expressedfrom, for example, the pol III U6 promoter, or another promoter (see,e.g., Stewart, et al. (2003) RNA April; 9(4):493-501, incorporated byreference herein in its entirety). The target gene or sequence of theRNA interfering agent may be a cellular gene or genomic sequence, e.g.the MDM2 sequence. An siRNA may be substantially homologous to thetarget gene or genomic sequence, or a fragment thereof. As used in thiscontext, the term “homologous” is defined as being substantiallyidentical, sufficiently complementary, or similar to the target mRNA, ora fragment thereof, to effect RNA interference of the target. Inaddition to native RNA molecules, RNA suitable for inhibiting orinterfering with the expression of a target sequence includes RNAderivatives and analogs. Preferably, the siRNA is identical to itstarget. The siRNA preferably targets only one sequence. Each of the RNAinterfering agents, such as siRNAs, can be screened for potentialoff-target effects by, for example, expression profiling. Such methodsare known to one skilled in the art and are described, for example, inJackson et al. Nature Biotechnology 6:635-637, 2003, incorporated byreference herein in its entirety. In addition to expression profiling,one may also screen the potential target sequences for similar sequencesin the sequence databases to identify potential sequences which may haveoff-target effects. For example, according to Jackson et al. (NatureBiotechnology 6:635-637, 2003), fifteen, or perhaps as few as elevencontiguous nucleotides, of sequence identity are sufficient to directsilencing of non-targeted transcripts. Therefore, one may initiallyscreen the proposed siRNAs to avoid potential off-target silencing usingthe sequence identity analysis by any known sequence comparison methods,such as BLAST. siRNA sequences are chosen to maximize the uptake of theantisense (guide) strand of the siRNA into RISC and thereby maximize theability of RISC to target human GGT mRNA for degradation. siRNAmolecules need not be limited to those molecules containing only RNA,but, for example, further encompasses chemically modified nucleotidesand non-nucleotides, and also include molecules wherein a ribose sugarmolecule is substituted for another sugar molecule or a molecule whichperforms a similar function. Moreover, a non-natural linkage betweennucleotide residues can be used, such as a phosphorothioate linkage. TheRNA strand can be derivatized with a reactive functional group of areporter group, such as a fluorophore. Particularly useful derivativesare modified at a terminus or termini of an RNA strand, typically the 3′terminus of the sense strand. For example, the 2′-hydroxyl at the 3′terminus can be readily and selectively derivatized with a variety ofgroups. Other useful RNA derivatives incorporate nucleotides havingmodified carbohydrate moieties, such as 2′O-alkylated residues or2′-O-methyl ribosyl derivatives and 2′-O-fluoro ribosyl derivatives.

The RNA bases may also be modified in the RNAi compounds providedherein. Any modified base useful for inhibiting or interfering with theexpression of a target sequence may be used. For example, halogenatedbases, such as 5-bromouracil and 5-iodouracil can be incorporated. Thebases may also be alkylated, for example, 7-methylguanosine can beincorporated in place of a guanosine residue. Non-natural bases thatyield successful inhibition can also be incorporated. siRNAmodifications amenable for use with the present invention include2′-deoxy-2′-fluorouridine or locked nucleic acid (LNA) nucleotides andRNA duplexes containing either phosphodiester or varying numbers ofphosphorothioate linkages. Such modifications are known to one skilledin the art and are described, for example, in Braasch et al.,Biochemistry, 42: 7967-7975, 2003, incorporated by reference herein inits entirety. Most of the useful modifications to the siRNA moleculescan be introduced using chemistries established for antisenseoligonucleotide technology. In one embodiment, the modifications involveminimal 2′-O-methyl modification, preferably excluding suchmodification. Modifications also preferably exclude modifications of thefree 5′-hydroxyl groups of the siRNA.

In some embodiments, the compound provided in the compositions anddelivered via the methods described herein is a microRNA (miR). The miRcan be an endogenous miR or artificial miR (referred to herein as amiRNA mimic or miR-mim). An endogenous miR is a small RNA naturallypresent in the genome which is capable of modulating the productiveutilization of mRNA. An artificial miR includes any type of RNAsequence, other than endogenous miR, which is capable of modulating theproductive utilization of mRNA.

In some embodiments, the miR is miR-660 (SEQ ID NO:2 or SEQ ID NO:3) ora functional variant thereof. In some embodiments, the miR functionalvariant is at least 98% identical in sequence to either SEQ ID NO:2 orSEQ ID NO:3. In some embodiments, the miR functional variant is at least95% identical in sequence to SEQ ID NO:2 or SEQ ID NO:3. In someembodiments, the miR functional variant is at least 90% identical insequence to either SEQ ID NO:2 or SEQ ID NO:3. In some embodiments, themiR functional variant is at least 85% identical in sequence to SEQ IDNO:2 or SEQ ID NO:3. In some embodiments, the miR functional variant isat least 80% identical in sequence to SEQ ID NO:2 or SEQ ID NO:3.

In yet another embodiment of the invention, the compound that reducesthe expression level of MDM2 is an antisense oligonucleotidecomplementary to the MDM2 gene.

In some embodiments, the compound comprises the sequence 5′-ACCCAUU-3′(SEQ ID NO: 4) or 5′-ACCCATT-3′ (SEQ ID NO: 5). As established in theExample herein, a miR-660 (SEQ ID NO:2) targets the sequence5′-AAUGGGU-3′ (SEQ ID NO: 6) on MDM2, through the miR-660 complementarysequence 5′-ACCCAUU-3′ (SEQ ID NO: 4). That MDM2 sequence is thus aneffective antisense target and other antisense molecules that have5′-ACCCAUU-3′ (SEQ ID NO: 4) or 5′-ACCCATT-3′ (SEQ ID NO: 5) can beeffective in reducing expression of MDM2. Thus, the present invention inone embodiment includes a composition comprising an MDM2 antisenseinhibitor comprising the sequence 5′-ACCCAUU-3′ (SEQ ID NO: 4) or5′-ACCCATT-3′ (SEQ ID NO: 5).

In some embodiments, the MDM2 antisense inhibitor comprises one or moremodified nucleotides such that the antisense inhibitor is stable in ahuman longer than an antisense inhibitor that does not comprise the oneor more modified nucleotides. In other embodiments, the MDM2 antisenseinhibitor comprises SEQ ID NO: 2 or SEQ ID NO: 3, or a functionalvariant thereof.

In some embodiments, the compositions provided herein comprise a miR-660comprising one or more modified nucleotides such that the miR-660 isstable in a human longer than a miR-660 that does not comprise the oneor more modified nucleotides.

In one embodiment, the nucleic acid compound includes a modification toone or more of the nucleotides. Modifications can be made to the nucleicacid such that the modified nucleic acid is stable in a human longerthan the nucleic acid that does not comprise said modification. Forexample, the nucleic acid compound can be modified to comprise one ormore modified nucleotides (e.g., 1, 2, 3, 4, or more). Methods ofmodifying a nucleic acid to enhance its stability are known in the art,for example, such as those disclosed in U.S. Pat. No. 7,579,451, U.S.Patent Publications 2014/0179771 and 2014/0179763, the contents of eachof which are incorporated herein by reference. In some embodimentsprovided herein, the compound is a miR-660 comprising one or moremodified nucleotides such that the miR-660 is stable in a human longerthan a miR-660 that does not comprise the one or more modifiednucleotides.

In some embodiments, the compound is a peptide or peptidomimetic, or asmall molecule which inhibits activity of the MDM2 protein, e.g., asmall molecule which inhibits a protein-protein interaction between theMDM2 protein and p53, or an aptamer which inhibits expression oractivity of the MDM2 protein.

In some embodiments, the compound described herein is encoded by avector such as a viral vector or plasmid based expression vector. Afterthe administration of the vector to the patient, the compound in oneembodiment is expressed endogenously inside the patient. As used herein,the term “vector” refers to a nucleic acid molecule capable oftransporting another nucleic acid to which it has been linked. In oneembodiment, the vector includes a polyadenylation sequence, one or morerestriction sites, as well as one or more selectable markers such asneomycin phosphotransferase, hygromycin phosphotransferase orpuromycin-Nacetyl-transferase. Additionally, depending on the host cellchosen and the vector employed, other genetic elements such as an originof replication, additional nucleic acid restriction sites, enhancers,sequences conferring inducibility of transcription, and selectablemarkers, may also be incorporated into the vectors described herein.

Examples of commercially available plasmid-based expression vectors forRNAi compounds include but are not limited to members of the pSilencerseries (Ambion, Austin, Tex.) and pCpG-siRNA (InvivoGen, San Diego,Calif.). Viral vectors for expression of interfering RN may be derivedfrom a variety of viruses including adenovirus, adeno-associated virus,lentivirus (e.g., HIV, FIV, and EIAV), and herpes virus. Examples ofcommercially available viral vectors for shRNA expression includepSilencer adeno (Ambion, Austin, Tex.) and pLenti6/BLOCKiT™-DEST(Invitrogen, Carlsbad, Calif.). Selection of viral vectors, methods forexpressing the interfering RNA from the vector and methods of deliveringthe viral vector are within the ordinary skill of the art. Examples ofkits for production of PCR-generated shRNA expression cassettes includeSilencer Express (Ambion, Austin, Tex.) and siXpress (Mirus, Madison,Wis.).

One type of vector is a “plasmid”, which refers to a circular doublestranded DNA loop into which additional nucleic acid segments can beligated. Another type of vector is a viral vector, wherein additionalnucleic acid segments can be ligated into the viral genome. Certainvectors are capable of autonomous replication in a host cell into whichthey are introduced (e.g., bacterial vectors having a bacterial originof replication and episomal mammalian vectors). Other vectors (e.g.,non-episomal mammalian vectors) are integrated into the genome of a hostcell upon introduction into the host cell, and thereby are replicatedalong with the host genome. Moreover, certain vectors are capable ofdirecting the expression of genes to which they are operatively linked.Such vectors are referred to herein as “recombinant expression vectors”,or more simply “expression vectors.” In general, expression vectors ofutility in recombinant DNA techniques are often in the form of plasmids.Non-limiting examples of viral vectors include replication defectiveretroviruses, lentiviruses, adenoviruses and adeno-associated viruses(AAV). In some embodiments, a vector capable of expressing miR-660 whentransfected into a human cell is provided. In some of these embodiments,the vector is a viral vector.

In various embodiments, the miR-660 is administered to the patient suchthat it is expressed from a vector in a cell of the patient. See, e.g.,Example, using a lentiviral vector. Non-limiting examples of othervectors include other engineered viruses, plasmids, and mammalianexpression vectors.

Importantly, and as evident from the disclosure set forth above, thecompositions of the invention and the methods for treating a cancerpatient, e.g., by reducing MDM2 expression or MDM2 activity level orMDM2 interaction with p53 in the patient's tumor tissue (e.g., lungtumor tissue) are not limited to any particular compound. Examples ofsuch treatments include use of small molecule inhibitors (see, e.g.,Zhao et al., 2013), peptides (U.S. Pat. No. 8,598,127), antibodies(Weisbart et al., 2012), antisense (see, e.g., Chen et al., 1999, usingphosphorothionate nucleotide analogs), or administration of RNAicompounds such as miR-660.

Without wishing to be bound by theory, the administration of a miR-660(e.g., of SEQ ID NO: 2) can be considered to be an MDM2 antisensetreatment. In one embodiment, the miR-660, e.g., of SEQ ID NO: 2 targetsa specific sequence (AAUGGGU (SEQ ID NO: 6)) in the 3′UTR of MDM2 mRNA(see Example below and FIGS. 4A-4B). Thus, an antisense molecule havingthe sequence ACCCAUU (SEQ ID NO: 4) (or ACCCATT (SEQ ID NO: 5) for DNA)without wishing to be bound by theory, would likely inhibit MDM2production (and MDM2-mediated inhibition of p53) since miR-660 inhibitsMDM2 production with that sequence.

As provided throughout, in one aspect, the present invention provides apharmaceutical composition comprising the compound described herein anda pharmaceutically acceptable carrier. In one embodiment, thepharmaceutical composition comprises miR-660 or a functional variantthereof, e.g., a variant having one or more modified nucleotides, and apharmaceutically acceptable carrier.

Pharmaceutically acceptable carriers amenable for use herein arecovalently or non-covalently bound, admixed, encapsulated, conjugated,operably-linked, or otherwise associated with the therapeutic agent suchthat the pharmaceutically acceptable carrier stabilizes or increases thecellular uptake, stability, solubility, half-life, binding efficacy,specificity, targeting, distribution, absorption, or renal clearance ofthe agent. Alternatively, or in addition, the pharmaceuticallyacceptable carrier increases or decreases the immunogenicity of thecompound or allows for greater ease of administration of the compound.In one embodiment, the pharmaceutically acceptable carrier may becapable of increasing the cytotoxicity of the agent with respect to thetargeted cancer cells.

Alternatively, or in addition, a pharmaceutically acceptable carrieramenable for use herein is a salt (for example, acid addition salts,e.g., salts of hydrochloric, hydrobromic, acetic acid, and benzenesulfonic acid), esters, salts of such esters, or any other compoundwhich, upon administration to a subject, are capable of providing(directly or indirectly) the biologically active compositions of theinvention. As such, the invention encompasses prodrugs, and otherbioequivalents. As used herein, the term “prodrug” is a pharmacologicalsubstance that is administered in an inactive (or significantly lessactive) form. Once administered, the prodrug is metabolized in vivo intoan active metabolite. Pharmaceutically acceptable carriers arealternatively or additionally diluents, excipients, adjuvants,emulsifiers, buffers, stabilizers, and/or preservatives.

Pharmaceutically acceptable carriers of the invention are therapeuticagent delivery systems/mechanisms that increase uptake of the agent bytargeted cells. Non-limiting examples of pharmaceutically acceptablecarriers include liposomes, cationic lipids, anionic lipids, cationicpolymers, polymers, hydrogels, micro- or nano-capsules (biodegradable),microspheres (optionally bioadhesive), cyclodextrins, or any combinationof the preceding elements (see PCT Publication No. WO 00/53722; U.S.Patent Publication 2008/0076701, each of which is incorporated byreference herein in its entirety). Moreover, pharmaceutically acceptablecarriers that increase cellular uptake can be modified withcell-specific proteins or other elements such as receptors, ligands,antibodies to specifically target cellular uptake to a chosen cell type.

In one embodiment of the invention, compositions are first introducedinto a cell or cell population that is subsequently administered to asubject. In some embodiments, the agent is delivered intracellularly,e.g., in cells of a target tissue such as lung, or in inflamed tissues.Included within the invention are compositions and methods for deliveryof the agent composition by removing cells of a subject, delivering theisolated agent composition to the removed cells, and reintroducing thecells into a subject. In some embodiments, the compound described herein(e.g., miR-660) is combined with a cationic lipid or transfectionmaterial such as LIPOFECTAMINE (Invitrogen).

In one embodiment, the compound that reduces the activity or expressionof MDM2, or the interaction of MDM2 with p53, is prepared with apharmaceutically acceptable carrier(s) that protects the compoundagainst rapid elimination from the body, such as a controlled releaseformulation, including implants and microencapsulated delivery systems.Biodegradable, biocompatible polymers can be used as carriers, such asethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen,polyorthoesters, and polylactic acid. Methods for preparation of suchformulations will be apparent to those skilled in the art. Examples ofmaterials which can form hydrogels include polylactic acid, polyglycolicacid, PLGA polymers, alginates and alginate derivatives, gelatin,collagen, agarose, natural and synthetic polysaccharides, poly-aminoacids such as polypeptides particularly poly(lysine), polyesters such aspolyhydroxybutyrate and poly-F-caprolactone, polyanhydrides,polyphosphazines, poly(vinyl alcohols), poly(alkylene oxides)particularly poly(ethylene oxides), poly(allylamines) (PAM),poly(acrylates), modified styrene polymers such aspoly(4-aminomethylstyrene), pluronic polyols, polyoxamers, poly(uronicacids), poly(vinylpyrrolidone) and copolymers of the above, includinggraft copolymers.

Liposomal suspensions (including liposomes targeted to infected cellswith monoclonal antibodies to viral antigens) can also be used aspharmaceutically acceptable carriers. These can be prepared according tomethods known to those skilled in the art, for example, as described inU.S. Pat. No. 4,522,811, incorporated by reference herein in itsentirety.

In one embodiment, a pharmaceutically acceptable carrier is one or morecationic lipids that are bound or associated with the miR-660 or otherRNAi compound. Alternatively, or in additionally, the miR-660 (or otherRNAi compound) is encapsulated or surrounded in cationic lipids, e.g.liposomes, for in vivo delivery. Exemplary cationic lipids include, butare not limited to, N41-(2,3-dioleoyloxy)propyliN,N,N-trimethylammoniumchloride (DOTMA); 1,2-bis(oleoyloxy)-3-3-(trimethylammonium)propane(DOTAP), 1,2-bis(dimyrstoyloxy)-3-3-(trimethylammonia)propane (DMTAP);1,2-dimyristyloxypropyl-3-dimethylhydroxyethylammonium bromide (DMRIE);dimethyldioctadecylammonium bromide (DDAB);3-(N—(N′,N′-dimethylaminoethane)carbamoyl)cholesterol (DC-Chol);3β-[N′,N′-diguanidinoethyl-aminoethane)carbamoyl cholesterol (BGTC);2-(2-(3-(bis(3-aminopropyl)amino)propylamino)acetamido)-N,N-ditetradecyla-cetamide(RPR209120); pharmaceutically acceptable salts thereof, and mixturesthereof. Further exemplary cationic lipids include, but are not limitedto, 1,2-dialkenoyl-sn-glycero-3-ethylphosphocholines (EPCs), such as1,2-dioleoyl-sn-glycero-3-ethylphosphocholine,1,2-distearoyl-sn-glycero-3-ethylphosphocholine,1,2-dipalmitoyl-sn-glycero-3-ethylphosphocholine, pharmaceuticallyacceptable salts thereof, and mixtures thereof.

Exemplary polycationic lipids include, but are not limited to,tetramethyltetrapalmitoyl spermine (TMTPS), tetramethyltetraoleylspermine (TMTOS), tetramethlytetralauryl spermine (TMTLS),tetramethyltetramyristyl spermine (TMTMS), tetramethyldioleyl spermine(TMDOS), pharmaceutically acceptable salts thereof, and mixturesthereof. Further exemplary polycationic lipids include, but are notlimited to,2,5-bis(3-aminopropylamino)-N-(2-(dioctadecylamino)-2-oxoethyl)pentanamid-e(DOGS);2,5-bis(3-aminopropylamino)-N-(2-(di(Z)-octadeca-9-dienylamino)-2-oxoethyl)pentanamide(DOGS-9-en);2,5-bis(3-aminopropylamino)-N-(2-(di(9Z,12Z)-octadeca-9,12-dienylamino)-2-oxoethyl)pentanamide(DLinGS); 3-beta-(N4-(N1,N8-dicarbobenzoxyspermidine)carbamoyl)chole-sterol (GL-67);(9Z,9yZ)-2-(2,5-bis(3-aminopropylamino)pentanamido)propane-1,3-diyl-dioct-adec-9-enoate(DOSPER);2,3-dioleyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propanamini-urntrifluoro-acetate (DOSPA); pharmaceutically acceptable salts thereof,and mixtures thereof.

Examples of cationic lipids amenable for use with the compositionsdescribed herein include but are not limited to those described in U.S.Pat. Nos. 4,897,355; 5,279,833; 6,733,777; 6,376,248; 5,736,392;5,334,761; 5,459,127; U.S. Patent Application Publication No.2005/0064595; U.S. Pat. Nos. 5,208,036; 5,264,618; 5,279,833; 5,283,185;5,753,613; and 5,785,992, the contents of which are incorporated byreference in their entireties for all purposes.

Pharmaceutically acceptable carriers of the invention also includenon-cationic lipids, such as neutral, zwitterionic, and anionic lipids.Exemplary non-cationic lipids amenable for use herein include, but arenot limited to, 1,2-Dilauroyl-sn-glycerol (DLG);1,2-Dimyristoyl-snglycerol (DMG); 1,2-Dipalmitoyl-sn-glycerol (DPG);1,2-Distearoyl-sn-glycerol (DSG);1,2-Dilauroyl-sn-glycero-3-phosphatidic acid (sodium salt; DLPA);1,2-Dimyristoyl-snglycero-3-phosphatidic acid (sodium salt; DMPA);1,2-Dipalmitoyl-sn-glycero-3-phosphatidic acid (sodium salt; DPPA);1,2-Distearoyl-sn-glycero-3-phosphatidic acid (sodium salt; DSPA);1,2-Diarachidoyl-sn-glycero-3-phosphocholine (DAPC);1,2-Dilauroyl-sn-glycero-3-phosphocholine (DLPC);1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC);1,2-Dipalmitoyl-sn-glycero-0-ethyl-3-phosphocholine (chloride ortriflate; DPePC); 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC);1,2-Distearoyl-sn-glycero-3-phosphocholine (DSPC);1,2-Dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE);1,2-Dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE);1,2-Dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE);1,2-Distearoylsn-glycero-3-phosphoethanolamine (DSPE);1,2-Dilauroyl-sn-glycero-3-phosphoglycerol (sodium salt; DLPG);1,2-Dimyristoyl-sn-glycero-3-phosphoglycerol (sodium salt; DMPG);1,2-Dimyristoyl-sn-glycero-3-phospho-sn-1-glycerol (ammonium salt;DMP-sn1-G); 1,2-Dipalmitoyl-sn-glycero-3-phosphoglycerol (sodium salt;DPPG); 1,2-Distearoyl-sn-glycero-3-phosphoglycero (sodium salt; DSPG);1,2-Distearoyl-snglycero-3-phospho-sn-1-glycerol (sodium salt;DSP-sn-1-G); 1,2-Dipalmitoyl-snglycero-3-phospho-L-serine (sodium salt;DPP S); 1-Palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine (PLinoPC);1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC);1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (sodium salt; POPG);1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (sodium salt; POPG);1-Palmitoyl-2-oleoyl-snglycero-3-phosphoglycerol (ammonium salt; POPG);1-Palmitoyl-2-4-o-sn-glycero-3-phosphocholine (P-lyso-PC);1-Stearoyl-2-lyso-sn-glycero-3-phosphocholine (S-lysoPC); and mixturesthereof. Further examplary non-cationic lipids include, but are notlimited to, polymeric compounds and polymer-lipid conjugates orpolymeric lipids, such as pegylated lipids, includingpolyethyleneglycols,N-(Carbonylmethoxypolyethyleneglycol-2000)-1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine(sodium salt; DMPE-MPEG-2000);N-(Carbonyl-methoxypolyethyleneglycol-5000)-1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine(sodium salt; DMPE-MPEG-5000); N(Carbonyl-methoxypolyethyleneglycol2000)-1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (sodium salt;DPPE-MPEG-2000); N-(Carbonyl-methoxypolyethyleneglycol5000)-1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (sodium salt;DPPE-MPEG-5000); N-(Carbonyl-methoxypolyethyleneglycol750)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine (sodium salt;DSPE-MPEG-750); N(Carbonyl-methoxypolyethyleneglycol2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine (sodium salt;DSPE-MPEG-2000); N-(Carbonylmethoxypolyethyleneglycol5000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine (sodium salt;DSPE-MPEG-5000); sodium cholesteryl sulfate (SCS); pharmaceuticallyacceptable salts thereof, and mixtures thereof. Examples of non-cationiclipids include, but are not limited to, dioleoylphosphatidylethanolamine(DOPE), diphytanoylphosphatidylethanolamine (DPhPE),1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (DOPC),1,2-Diphytanoyl-sn-Glycero-3-Phosphocholine (DPhPC), cholesterol, andmixtures thereof.

Pharmaceutically-acceptable carriers of the invention in one embodiment,include one or more anionic lipids. Exemplary anionic lipids include,but are not limited to, phosphatidylserine, phosphatidic acid,phosphatidylcholine, platelet-activation factor (PAF),phosphatidylethanolamine, phosphatidyl-DL-glycerol,phosphatidylinositol, phosphatidylinositol (pi(4)p, pi(4,5)p2),cardiolipin (sodium salt), lysophosphatides, hydrogenated phospholipids,sphingoplipids, gangliosides, phytosphingosine, sphinganines,pharmaceutically acceptable salts thereof, and mixtures thereof.

Another aspect of the invention relates to the treatment of a cancerpatient, e.g., a lung cancer patient, with one or more of thecompositions described herein. For example, in one embodiment, a patientin need of treatment of lung cancer is administered a compositioncomprising a therapeutically effective amount of a composition thatreduces the activity or expression of MDM2, or the interaction of MDM2with p53. In a further embodiment, the compound is an MDM2 RNAicompound. In even a further embodiment, the compound is a miR-660.

Methods for delivering the therapeutic compositions for use herein aredescribed, e.g., in Akhtar, et al., Trends Cell Bio. 2:139, 1992;Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed.Akhtar, 1995; Maurer, et al., Mol. Membr. Biol. 16:129-140, 1999;Hofland and Huang, Handb. Exp. Pharmacol. 137:165-192, 1999; and Lee, etal., ACS Symp. Ser. 752:184-192, 2000, each of which is incorporated byreference herein in its entirety for all purposes. International PCTPublication No. WO 94/02595 further describes general methods fordelivery of enzymatic nucleic acid molecules. These protocols can beutilized to supplement or complement delivery of the agent.

Pharmaceutical compositions can be administered locally and/orsystemically. As used herein, the term “local administration” is meantto describe the administration of a pharmaceutical composition of theinvention to a specific tissue or area of the body with minimaldissemination of the composition to surrounding tissues or areas.Locally administered pharmaceutical compositions are not detectable inthe general blood stream when sampled at a site not immediate adjacentor subjacent to the site of administration.

As used herein the term “systemic administration” is meant to describein vivo systemic absorption or accumulation of drugs in the blood streamfollowed by distribution throughout the entire body. Administrationroutes which lead to systemic absorption include, without limitation:intravenous, subcutaneous, intraperitoneal, inhalation, oral,intrapulmonary and intramuscular. Each of these administration routesexposes the therapeutic agent to an accessible diseased tissue. The rateof entry of a drug into the circulation has been shown to be a functionof molecular weight or size. The use of a liposome or other drug carriercomprising the compounds of the instant disclosure can potentiallylocalize the drug, e.g., in certain tissue types, such as the tissues ofthe reticular endothelial system (RES). A liposome formulation that canfacilitate the association of drug with the surface of cells, such as,lymphocytes and macrophages is also useful. This approach may provideenhanced delivery of the drug to target cells by taking advantage of thespecificity of macrophage and lymphocyte immune recognition of abnormalcells, such as cancer cells.

A pharmaceutically effective dose depends on the type of disease, thecomposition used, the route of administration, the individual andphysical characteristics of the subject under consideration (forexample, age, gender, weight, diet, smoking-habit, exercise-routine,genetic background, medical history, hydration, blood chemistry),concurrent medication, and other factors that those skilled in themedical arts will recognize.

Generally, an amount from about 0.01 mg/kg and 25 mg/kg body weight/dayof active ingredients is administered dependent upon potency of themiRNA and/or the miRNA inhibitor, e.g. the therapeutic composition. Inalternative embodiments dosage ranges include, but are not limited to,0.01-0.1 mg/kg, 0.01-1 mg/kg, 0.01-10 mg/kg, 0.01-20 mg/kg, 0.01-30mg/kg, 0.01-40 mg/kg, 0.01-50 mg/kg, 0.01-60 mg/kg, 0.01-70 mg/kg,0.01-80 mg/kg, 0.01-90 mg/kg, 0.01-100 mg/kg, 0.01-150 mg/kg, 0.01-200mg/kg, 0.01-250 mg/kg, 0.01-300 mg/kg, 0.01-500 mg/kg, and all rangesand points in between. In alternative embodiments dosage ranges include,but are not limited to, 0.01-1 mg/kg, 1-10 mg/kg, 10-20 mg/kg, 20-30mg/kg, 30-40 mg/kg, 40-50 mg/kg, 50-60 mg/kg, 60-70 mg/kg, 70-80 mg/kg,80-90 mg/kg, 90-100 mg/kg, 100-150 mg/kg, 150-200 mg/kg, 200-300 mg/kg,300-500 mg/kg, and all ranges and points in between.

A pharmaceutically acceptable carrier is chosen to be compatible withits intended route of administration. Examples of routes ofadministration include parenteral, e.g., intravenous, intradermal,subcutaneous, oral (e.g., inhalation or insufflation), transdermal(topical), transmucosal, transopthalmic, tracheal, intranasal,epidermal, intraperitoneal, intraorbital, intraarterial, intracapsular,intraspinal, intrasternal, intracranial, intrathecal, intraventricular,and rectal administration. Alternatively, or in addition, compositionsof the invention are administered non-parentally, for example, orally.Alternatively, or further in addition, compositions of the invention areadministered surgically, for example, as implants or biocompatiblepolymers.

Pharmaceutical compositions are administered via injection or infusion,e.g. by use of an infusion pump. Direct injection of the nucleic acidmolecules of the invention, is performed using standard needle andsyringe methodologies, or by needle-free technologies such as thosedescribed in Conry et al., Clin. Cancer Res. 5:2330-2337, 1999 andInternational PCT Publication No. WO 99/31262, each of which isincorporated by reference herein in its entirety.

Solutions or suspensions used for parenteral, intradermal, orsubcutaneous application can include the following components: a sterilediluent such as water for injection, saline solution, fixed oils,polyethylene glycols, glycerine, propylene glycol or other syntheticsolvents; antibacterial agents such as benzyl alcohol or methylparabens; antioxidants such as ascorbic acid or sodium bisulfate;chelating agents such as ethylenediaminetetraacetic acid; buffers suchas acetates, citrates or phosphates, and agents for the adjustment oftonicity such as sodium chloride or dextrose. The pH can be adjustedwith acids or bases, such as hydrochloric acid or sodium hydroxide. Theparenteral preparation can be enclosed in ampoules, disposable syringesor multiple dose vials made of glass or plastic.

An isolated agent with a pharmaceutically acceptable carrier of theinvention can be administered to a subject in many of the well-knownmethods currently used for chemotherapeutic treatment. For example, fortreatment of cancers, a compound of the invention may be injecteddirectly into tumors, injected into the blood stream or body cavities ortaken orally or applied through the skin with patches. The dose chosenshould be sufficient to constitute effective treatment but not so highas to cause unacceptable side effects. The state of the diseasecondition (e.g., cancer, precancer, and the like) and the health of thesubject should preferably be closely monitored during and for areasonable period after treatment.

In one embodiment, compositions suitable for injectable use includesterile aqueous solutions (where water soluble) or dispersions andsterile powders for the extemporaneous preparation of sterile injectablesolutions or dispersion. For intravenous administration, suitablecarriers include physiological saline, bacteriostatic water, CremophorEL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In allcases, the composition must be sterile and should be fluid to the extentthat easy syringeability exists. It must be stable under the conditionsof manufacture and storage and must be preserved against thecontaminating action of microorganisms such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (for example, glycerol, propylene glycol, andliquid polyethylene glycol, and the like), and suitable mixturesthereof.

The pharmaceutical compositions can be in the form of a sterileinjectable aqueous or oleaginous suspension. This suspension isformulated according to the known art using those suitable dispersing orwetting agents and suspending agents that have been mentioned above. Thesterile injectable preparation is a sterile injectable solution orsuspension in a non-toxic parentally acceptable diluent or solvent,e.g., as a solution in 1,3-butanediol. Exemplary acceptable vehicles andsolvents are water, Ringer's solution and isotonic sodium chloridesolution. In addition, sterile, fixed oils are conventionally employedas a solvent or suspending medium. For this purpose, any bland fixed oilis employed including synthetic mono- or diglycerides. In addition,fatty acids such as oleic acid are used in the preparation ofinjectables.

Sterile injectable solutions can be prepared by incorporating the agentin the required amount in an appropriate solvent with one or acombination of ingredients enumerated above, as required, followed byfiltered sterilization. Generally, dispersions are prepared byincorporating the active compound into a sterile vehicle that contains abasic dispersion medium and the required other ingredients from thoseenumerated above. In the case of sterile powders for the preparation ofsterile injectable solutions, methods of preparation are vacuum dryingand freeze-drying that yields a powder of the active ingredient plus anyadditional desired ingredient from a previously sterile-filteredsolution thereof.

Oral compositions generally include an inert diluent or an ediblepharmaceutically acceptable carrier. Agents containing at least one2′-O-methoxyethyl modification are used when formulating compositionsfor oral administration. They can be enclosed in gelatin capsules orcompressed into tablets. For the purpose of oral therapeuticadministration, the active compound can be incorporated with excipientsand used in the form of tablets, troches, or capsules. Oral compositionscan also be prepared using a fluid carrier for use as a mouthwash,wherein the compound in the fluid carrier is applied orally and swishedand expectorated or swallowed. Pharmaceutically compatible bindingagents, and/or adjuvant materials can be included as part of thecomposition. The tablets, pills, capsules, troches and the like cancontain any of the following ingredients, or compounds of a similarnature: a binder such as microcrystalline cellulose, gum tragacanth orgelatin; an excipient such as starch or lactose, a disintegrating agentsuch as alginic acid, Primogel, or corn starch; a lubricant such asmagnesium stearate or Sterotes; a glidant such as colloidal silicondioxide; a sweetening agent such as sucrose or saccharin; or a flavoringagent such as peppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds are delivered in theform of an aerosol spray from pressured container or dispenser, whichcontains a suitable propellant, e.g., a gas such as carbon dioxide, or anebulizer.

Systemic administration can also be by transmucosal or transdermalmeans. For transmucosal or transdermal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Exemplary penetrants for transdermal administration include, but are notlimited to, lipids, liposomes, fatty acids, fatty acid, esters,steroids, chelating agents, and surfactants. Preferred lipids andliposomes of the invention are neutral, negative, or cationic.Compositions are encapsulated within liposomes or form complexesthereto, such as cationic liposomes.

Alternatively, or additionally, the compound is complexed to one or morelipids, such as one or more cationic lipids, e.g., in the form of alipid nanoparticle or liposome. Compositions prepared for transdermaladministration in one embodiment are provided by iontophoresis. Suchpenetrants are generally known in the art, and include, for example, fortransmucosal administration, detergents, bile salts, and fusidic acidderivatives.

Transmucosal administration can be accomplished through the use of nasalsprays or suppositories. For transdermal administration, the activecompounds are formulated into patches, ointments, lotions, salves, gels,drops, sprays, liquids, powders, or creams as generally known in theart.

Other non-limiting examples of delivery strategies for the therapeuticagents of the instant disclosure include material described in Boado, etal., J. Pharm. Sci. 87:1308-1315, 1998; Tyler, et al., FEBS Lett.421:280-284, 1999; Pardridge, et al, PNAS USA. 92:5592-5596, 1995;Boado, Adv. Drug Delivery Rev. 15:73-107, 1995; Aldrian-Herrada, et al.,Nucleic Acids Res. 26:4910-4916, 1998; and Tyler, et al., PNAS USA.96:7053-7058, 1999, the contents of each of which are incorporated byreference herein in their entireties.

The compositions of the invention may also be administered in the formof suppositories, e.g., for rectal administration of the drug. Thesecompositions are prepared by mixing the drug with a suitablenon-irritating excipient that is solid at ordinary temperatures butliquid at the rectal temperature and will therefore melt in the rectumto release the drug. Such materials include cocoa butter andpolyethylene glycols.

Aqueous suspensions contain the active materials in admixture withexcipients suitable for the manufacture of aqueous suspensions. Suchexcipients are suspending agents, e.g., sodium carboxymethylcellulose,methylcellulose, hydropropylmethylcellulose, sodium alginate,polyvinylpyrrolidone, gum tragacanth and gum acacia; dispersing orwetting agents can be a naturally-occurring phosphatide, e.g., lecithin,or condensation products of an alkylene oxide with fatty acids, e.g.,polyoxyethylene stearate, or condensation products of ethylene oxidewith long chain aliphatic alcohols, e.g., heptadecaethyleneoxycetanol,or condensation products of ethylene oxide with partial esters derivedfrom fatty acids and a hexitol such as polyoxyethylene sorbitolmonooleate, or condensation products of ethylene oxide with partialesters derived from fatty acids and hexitol anhydrides, e.g.,polyethylene sorbitan monooleate. The aqueous suspensions also containone or more preservatives, e.g., ethyl, or n-propyl p-hydroxybenzoate,one or more coloring agents, one or more flavoring agents, and one ormore sweetening agents, such as sucrose or saccharin.

Oily suspensions are formulated by suspending the active ingredients ina vegetable oil, e.g., arachis oil, olive oil, sesame oil or coconutoil, or in a mineral oil such as liquid paraffin. The oily suspensionscontain a thickening agent, e.g., beeswax, hard paraffin or cetylalcohol. Sweetening agents and flavoring agents are added to providepalatable oral preparations. These compositions are preserved by theaddition of an antioxidant such as ascorbic acid.

Dispersible powders and granules suitable for preparation of an aqueoussuspension by the addition of water provide the active ingredient inadmixture with a dispersing or wetting agent, suspending agent and oneor more preservatives. Suitable dispersing or wetting agents orsuspending agents are exemplified by those already mentioned above.Additional excipients, e.g., sweetening, flavoring and coloring agents,are also present.

Pharmaceutical compositions of the invention can be in the form ofoil-in-water emulsions. The oily phase is a vegetable oil or a mineraloil or mixtures of these. Suitable emulsifying agents arenaturally-occurring gums, e.g., gum acacia or gum tragacanth,naturally-occurring phosphatides, e.g., soy bean, lecithin, and estersor partial esters derived from fatty acids and hexitol, anhydrides,e.g., sorbitan monooleate, and condensation products of the said partialesters with ethylene oxide, e.g., polyoxyethylene sorbitan monooleate.The emulsions also contain sweetening and flavoring agents.

In a preferred aspect, the pharmaceutically acceptable carrier can be asolubilizing carrier molecule. More preferably, the solubilizing carriermolecule can be Poloxamer, Povidone K17, Povidone K12, Tween 80,ethanol, Cremophor/ethanol, Lipiodol, polyethylene glycol (PEG) 400,propylene glycol, Trappsol, alpha-cyclodextrin or analogs thereof,beta-cyclodextrin or analogs thereof, and gamma-cyclodextrin or analogsthereof.

The invention also provides compositions prepared for storage oradministration. Acceptable carriers or diluents for therapeutic use arewell known in the pharmaceutical art, and are described, e.g., inRemington's Pharmaceutical Sciences, Mack Publishing Co., A. R. GennaroEd., 1985. For example, preservatives, stabilizers, dyes and flavoringagents are provided. These include sodium benzoate, sorbic acid andesters of phydroxybenzoic acid. In addition, antioxidants and suspendingagents are used.

In one aspect, a composition provided herein is administered to a lungcancer patient in need of treatment. The lung cancer, in one embodiment,is small cell lung cancer. In another embodiment, the lung cancer isnon-small cell lung cancer (NSCLC). In a further embodiment, the NSCLCis adenocarcinoma, squamous cell carcinoma or large-cell lung cancer.

In one embodiment, the patient in need of treatment (i) expressesmiR-660 in a lung tissue sample or biological fluid sample at a levellower than a control level derived from a subject or plurality ofsubjects that do not have lung cancer, or as compared to a control levelderived from a lung cancer patient or plurality thereof, that have beengiven a favorable prognosis; (ii) expresses MDM2 at a higher level in alung tissue sample or biological fluid sample as compared to a controllevel derived from a subject or plurality of subjects that do not havelung cancer, or as compared to a control level derived from a lungcancer patient or plurality thereof that have been given a favorableprognosis; and/or (iii) expresses p53 in a lung tissue sample or abiological fluid sample below a control level derived from a lung tumortissue sample (or plurality thereof) or a biological fluid sample (orplurality thereof) obtained from a patient that has a favorable lungcancer prognosis; or a control level derived from a healthy subject.

In one embodiment of the methods of treatments described herein, apatient in need of treatment expresses p53 in a lung cancer tumor sampleobtained from the patient. In a further embodiment, the patient is inneed of treatment if the MDM2 expression level in the patient's sampleof lung tumor tissue is higher than an MDM2 expression level in anon-cancerous tissue sample obtained from the patient, or obtained froma different patient. In one embodiment, a patient in need of treatmentexpresses p53 in his or her lung tumor tissue sample below a p53expression level in a tissue sample from non-cancerous tissue obtainedfrom the patient (a control level).

In another embodiment, a patient is in need of treatment and thereforeadministered one of the compositions provided herein if the patient'slung tumor tissue has one or more of the following characteristics (i)p53 is present in a lung tumor tissue sample from the patient; (ii) theMDM2 expression level in the tumor tissue sample from the patient isabove an MDM2 expression level in non-cancerous tissue; (iii) themiR-660 concentration in the patient in a lung tissue sample orbiological fluid sample is below a miR-660 mean concentration controllevel derived from lung tissue samples or biological fluid samples froma plurality of control subjects that do not have lung cancer, or aplurality of lung cancer patients that have been given a favorableprognosis.

In some embodiments, the patient in need thereof is selected fortreatment based on the MDM2 expression level in a lung tumor tissuesample obtained from the patient or a biological fluid sample obtainedfrom the patient. The biological fluid sample, in one embodiment, isblood, serum, plasma, urine, saliva, mucus, tears, amniotic fluid,breast milk, sputum, cerebrospinal fluid, peritoneal fluid, pleuralfluid, seminal fluid, a fraction thereof or a combination thereof. Insome embodiments, the MDM2 expression level in a lung tumor tissuesample of the patient is above an MDM2 expression level in a lung tumortissue sample from a plurality of lung cancer patients that have afavorable prognosis. In some embodiments, the MDM2 expression level in alung tumor tissue sample of the patient is above an MDM2 expressionlevel in a noncancerous lung tissue sample from the patient. In oneembodiment, the MDM2 expression level in a lung tumor tissue sample ofthe patient is above an MDM2 expression level in a lung tissue samplefrom a healthy subject. In some embodiments, the MDM2 expression levelin a lung tumor tissue sample of the patient is above an average MDM2expression level in lung tissue samples from a plurality of healthysubjects.

In some embodiments, the patient in need thereof is selected fortreatment based on the miR-660 expression level in a lung tumor tissuesample or a biological fluid sample obtained from the patient. Thebiological fluid sample, in one embodiment, is blood, serum, plasma,urine, saliva, mucus, tears, amniotic fluid, breast milk, sputum,cerebrospinal fluid, peritoneal fluid, pleural fluid, seminal fluid, afraction thereof or a combination thereof.

In some embodiments, the miR-660 expression level in a lung tumor tissuesample of the patient is below a miR-660 expression level in anoncancerous lung tissue sample from the patient. In some embodiments,the miR-660 expression level in a lung tumor tissue sample of thepatient is below a miR-660 expression level in a lung tissue sample of asubject that does not have lung cancer (e.g., a healthy subject). Insome embodiments, the miR-660 expression level in a lung tumor tissuesample of the patient is below an average miR-660 expression level inlung tissue samples of a plurality of subjects that do not have lungcancer.

In some embodiments of this method, the miR-660 concentration is alsodetermined in the lung tumor tissue, and, if the miR-660 concentrationin the patient is below a miR-660 concentration in the same fluid ortissue of a plurality of lung cancer patients that had a favorableprognosis, the treatment of the patient is recommended, or the patientis treated by administering miR-660 to the patient in a mannersufficient to treat the lung cancer.

In some embodiments, the patient in need thereof id selected based onthe miR-660 expression level in a plasma or blood sample obtained fromthe patient. In some embodiments, the miR-660 expression level in aplasma or blood sample of the patient is below a miR-660 expressionlevel in a plasma or blood sample of a subject that does not have lungcancer (e.g., a healthy subject). In some embodiments, the miR-660expression level in a plasma sample of the patient is below an averagemiR-660 expression level in plasma samples of a plurality of subjectsthat do not have lung cancer.

Accordingly, in some embodiments, the methods for treating cancerprovided herein, e.g., lung cancer, comprise treating the patient insuch a manner as to increase the miR-660 concentration in the patient'slung tumor tissue, e.g., by administering a miR-660 to the patient inneed thereof. In some embodiments, the above treatment methods furthercomprise recommending treatment, or treating the patient with a therapythat increases miR-660 concentration in the patient's lung tumor tissue,if the patient has lung cancer. Non-limiting examples of such a therapyincludes administration of miR-660 and administration of a transient orstable vector that expresses miR-660.

Since miR-660 administration (and other therapies that reduce MDM2expression and/or activity, and/or MDM2 interaction with p53) iseffective against lung tumors when p53 is present (see Example), adetermination that p53 is present in the tumor tissue in one embodimentindicates that the patient could benefit from one of the compositionsdescribed herein, for example a composition comprising a therapeuticallyeffective amount of miR-660, to raise p53 to normal levels or above. Inone embodiment, p53 expression in a patient in need of treatment is ap53 expression level below normal p53 levels or below levels in patientsthat have a favorable prognosis.

Accordingly, in some embodiments, the patient in need of treatment isidentified or selected based on the p53 expression level in a lung tumortissue sample obtained from the patient. In some embodiments, the lungtumor tissue sample from the patient expresses p53. In some embodiments,the p53 expression level in a lung tumor tissue sample of the patient isbelow a p53 expression level in a noncancerous lung tissue sample fromthe patient. In some embodiments, the p53 expression level in a lungtumor tissue sample of the patient is below a p53 expression level in alung tissue sample of a subject that does not have lung cancer (e.g., ahealthy subject). In some embodiments, the p53 expression level in alung tumor tissue sample of the patient is below an average p53expression level in lung tissue samples of a plurality of subjects thatdo not have lung cancer or a plurality of lung cancer patients that havebeen given a favorable prognosis.

In some embodiments, the patient in need thereof can be selected basedon the p53 expression level in a biological fluid sample obtained fromthe patient. The biological fluid sample, in one embodiment, is blood,serum, plasma, urine, saliva, mucus, tears, amniotic fluid, breast milk,sputum, cerebrospinal fluid, peritoneal fluid, pleural fluid, seminalfluid, a fraction thereof or a combination thereof. In some embodiments,the biological fluid sample from the patient expresses p53. In someembodiments, the p53 expression level in a biological fluid sample ofthe patient is below a p53 expression level in a plasma sample of asubject that does not have lung cancer (e.g., a healthy subject). Insome embodiments, the p53 expression level in a biological fluid sampleof the patient is below an average p53 expression level in plasmasamples of a plurality of subjects that do not have lung cancer.

In some embodiments, the patient in need of treatment is selected basedon his or her p53 expression level and his or her miR-660 expressionlevel. In some embodiments, the patient in need thereof is selectedbased on the MDM2 expression level and the miR-660 expression level. Insome embodiments, the patient in need thereof can be selected based onthe p53 expression level and the MDM2 expression level. In someembodiments, the patient in need of treatment is selected based on theexpression levels of p53, MDM2, and miR-660.

In some embodiments of this method, the patient is treated with thetherapy if the concentration is below a miR-660 concentration in thesame fluid or tissue of a plurality of lung cancer patients that had afavorable prognosis. In other embodiments, the therapy that reduces theMDM2 expression level is administration of miR-660. In furtherembodiments, the patient is treated if the p53 expression level is belowa p53 expression level in a tissue sample from non-cancerous tissue,either from the patient or from another subject.

Patients can be selected for treatment with the compositions and methodsdescribed herein, for example, via one of the diagnostic methodsprovided in U.S. Patent Application Publication No. 2015/0191794, thecontents of which are incorporated by reference in their entirety forall purposes.

Specifically, U.S. Patent Application Publication No. 2015/0191794discloses 24 miRNAs and subsets thereof that can be assessed todetermine the presence of a pulmonary tumor in a subject. These 24miRNAs are shown in Table A. In one embodiment, expression of five ormore, ten or more, 15 or more, 20 or more or the 24 miRNAs shown inTable A are used to select a subject for treatment with one of thecompositions described herein.

TABLE A hsa-miR-16 hsa-miR-320 hsa-miR-148a hsa-miR-17 hsa-miR-451hsa-miR-15b hsa-miR-21 hsa-miR-660 hsa-miR-19b hsa-miR-101 hsa-miR-106ahsa-miR-28-3p hsa-miR-126 hsa-miR-133a hsa-miR-30b hsa-miR-145hsa-miR-140-3p hsa-miR-30c hsa-miR-197 hsa-miR-140-5p hsa-miR-486-5phsa-miR-221 hsa-miR-142-3p hsa-miR-92a

A summary of the miRNAs that can be used can be found in Table 2 of theU.S. Patent Application Publication No. 2015/0191794.

For example, in one embodiment, a reverse transcription polymerase chainreaction (RT-PCR) is performed on the at least 5 miRNAs with DNA primersand or DNA probes specific for the at least 5 miRNAs to form cDNAmolecules that correspond to the at least 5 miRNAs. The levels of thecDNA molecules that correspond to the at least 5 miRNAs are thendetected. Next, the levels of the cDNA molecules that correspond to theat least 5 miRNAs are compared to a sample training set. The sampletraining set in one embodiment comprises levels of the cDNA moleculesthat correspond to the at least 5 miRNAs from a reference normal sampleor a reference lung cancer sample (e.g., a reference NSCLC sample). Thepatient is selected for treatment based on the results of thiscomparison.

In another embodiment, the patient in need of treatment is identified bydetermining the expression ratio of a miRNA pair (or a pluralitythereof) in a biological sample from the patient. The expression ratiois compared with a cut-off value determined from the average ratio of aplurality of corresponding miRNA pairs from a plurality of controlsamples. Based on this comparison, a positive score for the expressionratio of the miRNA pair is assigned if the ratio exceeds the cut-offvalue. Additional miRNA pairs are analyzed in an identical fashion, inone embodiment, until either (1) at least nine miRNA pair expressionratios are assigned a positive score, or (2) after the comparison of theexpression ratios of 27 miRNA pairs, less than nine miRNA pairexpression ratios are assigned a positive score. In one embodiment,based on the number of positive scores, i.e., greater than or equal tonine, the patient is selected for therapy. The miRNA pairs, in oneembodiment, include 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p,133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21,142-3p/221, 142-3p/30b, and/or 320/660, or the inverse ratios thereof. Alung cancer tumor is identified (and a patient is selected fortreatment) if at least nine of the miRNA pair expression ratios areassigned a positive score. In another embodiment, the patient is notselected for therapy if less than nine miRNA pair expression ratios areassigned a positive score.

In some embodiments, the miRNA pairs include 106a/660, 106a/92a,126/660, 140-5p/197, 140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p,17/660, 17/92a, 197/660, 197/92a, 19b/660, 28-3p/660, or the inverseratios thereof.

For the evaluation of diagnostic and prognostic tests, predictive valueshelp interpret the results of tests in the clinical setting. Thediagnostic or prognostic value of a procedure is defined by itssensitivity, specificity, predictive value and efficiency. Any testmethod will produce True Positive (TP), False Negative (FN), FalsePositive (FP), and True Negative (TN). The “sensitivity” of a test isthe percentage of all patients with disease present or that do respondwho have a positive test or (TP/TP+FN)×100%. The “specificity” of a testis the percentage of all patients without disease or who do not respond,who have a negative test or (TN/FP+TN)×1100%. The “predictive value” or“PV” of a test is a measure (%) of the times that the value (positive ornegative) is the true value, i.e., the percent of all positive teststhat are true positives is the Positive Predictive Value (PV+) or(TP/TP+FP)×100%. The “negative predictive value” (PV) is the percentageof patients with a negative test who will not respond or(TN/FN+TN)×100%. The “accuracy” or “efficiency” of a test is thepercentage of the times that the test give the correct answer comparedto the total number of tests or (TP+TN/TP+TN+FP+FN)×100%. The “errorrate” calculates from those patients predicted to respond who did notand those patients who responded that were not predicted to respond or(FP+FN/TP+TN+FP+FN)×100%. The overall test “specificity” is a measure ofthe accuracy of the sensitivity and specificity of a test do not changeas the overall likelihood of disease changes in a population, thepredictive value does change. The PV changes with a physician's clinicalassessment of the presence or absence of disease or presence or absenceof clinical response in a given patient.

A predetermined “cutoff value” can be determined without undueexperimentation for any particular parameter, by evaluating patientsampling, treatment conditions and desired sensitivity and specificity.When numerical values from an individual test subject falls below thecutoff value, the subject is classified as falling into a one group orcategory, e.g. healthy, and when the numerical value, score, or ratiofalls above the cutoff, the subject is classified in the alternativegroup or category.

For any given test, the TP, FN, FP and TN can be determined and adjustedby the skilled artisan without undue experimentation by, e.g., adjustingthe cutoff value, adjusting the statistical significance (e.g., the Pvalue) for making a prognostic or diagnostic determination; adjustingthe accuracy of the test procedures, etc.

As demonstrated in the Example below, the concentration of miR-660 isdecreased in tissues or bodily fluids of lung cancer patients that havea poor prognosis, when compared to the concentration in patients thathave a favorable prognosis (FIG. 2A). Without being bound to anyparticular mechanism, it is believed that the patient has a poorprognosis as a consequence of the decreased miR-660, since miR-660interacts with MDM2, reducing MDM2 ability to down-regulate p53, andallowing p53 to suppress the tumor.

Thus, in some embodiments, a method of evaluating the prognosis of alung cancer patient is provided. The method comprises measuring theconcentration of miR-660 in a tissue sample or bodily fluid of thepatient, wherein a miR-660 concentration in the patient below a miR-660concentration in the same fluid or tissue of a plurality of lung cancerpatients that had a favorable prognosis indicates that the patient has apoor prognosis. In some of these methods, as described below, expressionlevels of MDM2 and/or p53 are measured as well.

In some embodiments of this method, the miR-660 expression level ismeasured in a tissue sample of the patient. MDM2 and/or p53 expressionlevels can also be determined from a tissue sample. With most of thesemethods, the tissue sample is a tumor tissue sample.

In some embodiments of this method, the miR-660 expression level ismeasured in a biological fluid sample obtained from the patient.Examples of biological fluid samples include, but are not limited to,blood, serum, plasma, urine, saliva, mucus, tears, amniotic fluid,breast milk, sputum, cerebrospinal fluid, peritoneal fluid, pleuralfluid, seminal fluid, a fraction thereof, or a combination thereof.

As used herein, a “tumor sample”, “tumor tissue sample”, “tumorcontaining sample”, “tumor cell containing sample”, or variationsthereof, refer to cell containing samples of tissue or fluid isolatedfrom an individual suspected of being afflicted with, or at risk ofdeveloping, cancer. The samples may contain tumor cells which may beisolated by known methods or other appropriate methods as deemeddesirable by the skilled practitioner. These include, but are notlimited to, microdissection, laser capture microdissection (LCM), orlaser microdissection (LMD) before use in the instant disclosure.Alternatively, undissected cells within a “section” of tissue may beused. Non-limiting examples of such samples include primary isolates (incontrast to cultured cells) and may be collected by any non-invasive,minimally invasive, or invasive means, including, but not limited to,ductal lavage, fine needle aspiration, needle biopsy, bronchoscopy, corebiopsy, thoracentesis, thoracotomy, the devices and methods described inU.S. Pat. No. 6,328,709, or any other suitable means recognized in theart.

For practicing the invention methods, the tissue can be prepared in anymanner that maintains the miRNA or protein concentration at least untilthe sample is utilized in the invention methods. Non-limiting usefultissue preparations include fresh, fresh-frozen, and formalinfixed/paraffin embedded (“FFPE”). See U.S. Pat. Nos. 7,364,846,7,723,039, 7,879,555 and 8,012,688 for methods that are useful inevaluating FFPE samples, each of these patents is incorporated byreference in its entirety.

In additional embodiments, the invention methods may be practiced byanalyzing miRNA and/or mRNA from single cells or homogenous cellpopulations which have been dissected away from, or otherwise isolatedor purified from, contaminating cells of a sample as present in a simplebiopsy. One advantage provided by these embodiments is thatcontaminating, non-tumor cells (such as infiltrating lymphocytes orother immune system cells) may be removed as so be absent from affectingthe nucleic acids identified or the subsequent analysis of miRNA or mRNAexpression levels as provided herein. Such contamination is presentwhere a biopsy is used to generate gene expression profiles.

In various embodiments of the invention methods, miR-660 or mRNA ismeasured in a bodily fluid of a patient. These embodiments are notnarrowly limited to any particular bodily fluid, since miRNA and mRNA ispresent in essentially all bodily fluids (Weber et al., 2010; De Guireet al., 2013; see also Rodriguez-Dorantes et al. 2014). Examples ofuseful bodily fluids are peripheral blood, serum, plasma, ascites,urine, sputum, saliva, broncheoalveolar lavage fluid, cyst fluid,pleural fluid, peritoneal fluid, lymph, pus, lavage fluids from sinuscavities, bronchopulmonary aspirates, and bone marrow aspirates. Theskilled artisan can determine, without undue experimentation, whetherany particular bodily fluid is useful for any particular application.

The concentration of the miRNAs provided herein (e.g., of SEQ ID NOs:2-3, Table A, miR-660, MDM2, p53, etc.) can be determined by anyreliable, sensitive, and specific method known in the art. In someembodiments, the protein level of miR-660, or MDM2 or p53 is measured.In some embodiments, the mRNA level miR-660, or MDM2 or p53 is measured.

In some embodiments of the invention methods, miR-660, or MDM2 or p53mRNA, is amplified prior to measurement. In other embodiments, the levelof those nucleic acids is measured during the amplification process. Instill other methods, the nucleic acids are not amplified prior tomeasurement.

Many methods exist for amplifying miRNA nucleic acid sequences such asmature miRNAs, precursor miRNAs, and primary miRNAs, as well as mRNAs.Suitable nucleic acid polymerization and amplification techniquesinclude reverse transcription (RT), polymerase chain reaction (PCR),real-time PCR (quantitative PCR (q-PCR)), nucleic acid sequence-baseamplification (NASBA), ligase chain reaction, multiplex ligatable probeamplification, invader technology (Third Wave), rolling circleamplification, in vitro transcription (IVT), strand displacementamplification, transcription-mediated amplification (TMA), RNA(Eberwine) amplification, and other methods that are known to personsskilled in the art. In certain embodiments, more than one amplificationmethod is used, such as reverse transcription followed by real timequantitative PCR (qRT-PCR).

In PCR and q-PCR methods, for example, a set of primers is used for eachtarget sequence. In certain embodiments, the lengths of the primersdepends on many factors, including, but not limited to, the desiredhybridization temperature between the primers, the target nucleic acidsequence, and the complexity of the different target nucleic acidsequences to be amplified. In certain embodiments, a primer is about 15to about 35 nucleotides in length. In other embodiments, a primer isequal to or fewer than 15, 20, 25, 30, or 35 nucleotides in length. Inadditional embodiments, a primer is at least 35 nucleotides in length.

In a further aspect, a forward primer can comprise at least one sequencethat anneals to a miRNA or mRNA and alternatively can comprise anadditional 5′ non-complementary region. In another aspect, a reverseprimer can be designed to anneal to the complement of a reversetranscribed miRNA or mRNA. The reverse primer may be independent of themiRNA or mRNA sequence, and multiple miRNA and mRNA biomarkers may beamplified using the same reverse primer. Alternatively, a reverse primermay be specific for a miRNA or mRNA biomarker.

The qRT-PCR reaction may further be combined with the reversetranscription reaction by including both a reverse transcriptase and aDNA-based thermostable DNA polymerase. When two polymerases are used, a“hot start” approach may be used to maximize assay performance (U.S.Pat. Nos. 5,411,876 and 5,985,619, incorporated by reference in theirentireties). For example, the components for a reverse transcriptasereaction and a PCR reaction may be sequestered using one or morethermoactivation methods or chemical alteration to improvepolymerization efficiency (U.S. Pat. Nos. 5,550,044, 5,413,924, and6,403,341, incorporated by reference in their entireties).

In certain embodiments, labels, dyes, or labeled probes and/or primersare used to detect amplified or unamplified miRNAs or mRNAs. The skilledartisan will recognize which detection methods are appropriate based onthe sensitivity of the detection method and the abundance of the target.Depending on the sensitivity of the detection method and the abundanceof the target, amplification may or may not be required prior todetection. One skilled in the art will recognize the detection methodswhere miRNA or mRNA amplification is employed.

A probe or primer may include Watson-Crick bases or modified bases.Modified bases include, but are not limited to, the AEGIS bases (fromEragen Biosciences), which have been described, e.g., in U.S. Pat. Nos.5,432,272, 5,965,364, and 6,001,983, incorporated by reference in theirentireties. In certain aspects, bases are joined by a naturalphosphodiester bond or a different chemical linkage. Different chemicallinkages include, but are not limited to, a peptide bond or a LockedNucleic Acid (LNA) linkage, which is described, e.g., in U.S. Pat. No.7,060,809, incorporated by reference in its entirety.

In a further embodiment, oligonucleotide probes or primers present in anamplification reaction are suitable for monitoring the amount ofamplification product produced as a function of time. In certainaspects, probes having different single stranded versus double strandedcharacter are used to detect the nucleic acid. Probes include, but arenot limited to, the 5′-exonuclease assay (e.g., TaqMan™) probes (seeU.S. Pat. No. 5,538,848, incorporated by reference in its entirety),stem-loop molecular beacons (see, e.g., U.S. Pat. Nos. 6,103,476 and5,925,517, incorporated by reference in their entireties), stemless orlinear beacons (see, e.g., WO 9921881, U.S. Pat. Nos. 6,485,901 and6,649,349), peptide nucleic acid (PNA) Molecular Beacons (see, e.g.,U.S. Pat. No. 6,355,421, incorporated by reference in its entirety andU.S. Pat. No. 6,593,091, incorporated by reference in its entirety),linear PNA beacons (see, e.g. U.S. Pat. No. 6,329,144, incorporated byreference in its entirety), non-FRET probes (see, e.g., U.S. Pat. No.6,150,097, incorporated by reference in its entirety),Sunrise™/AmplifluorB™ probes (see, e.g., U.S. Pat. No. 6,548,250,incorporated by reference in its entirety), stem-loop and duplexScorpion™ probes (see, e.g., U.S. Pat. No. 6,589,743, incorporated byreference in its entirety), bulge loop probes (see, e.g., U.S. Pat. No.6,590,091, incorporated by reference in its entirety), pseudo knotprobes (see, e.g., U.S. Pat. No. 6,548,250, incorporated by reference inits entirety), cyclicons (see, e.g., U.S. Pat. No. 6,383,752,incorporated by reference in its entirety), MGB Eclipse™ probe (EpochBiosciences), hairpin probes (see, e.g., U.S. Pat. No. 6,596,490,incorporated by reference in its entirety), PNA light-up probes,antiprimer quench probes (Li et al., Clin. Chem. 53:624-633 (2006),incorporated by reference in its entirety), self-assembled nanoparticleprobes, and ferrocene-modified probes described, for example, in U.S.Pat. No. 6,485,901, incorporated by reference in its entirety.

In certain embodiments, one or more of the primers in an amplificationreaction can include a label. In yet further embodiments, differentprobes or primers comprise detectable labels that are distinguishablefrom one another. In some embodiments a nucleic acid, such as the probeor primer, may be labeled with two or more distinguishable labels.

In some embodiments, the concentration of miR-660 and/or MDM2 and/or p53mRNA and/or one or more other miRNAs provided herein, e.g., one or moremiRNAs from the panel set forth at Table A, is measured using amicroarray or another support.

A “microarray” is a linear or two-dimensional or three dimensional (andsolid phase) array of discrete regions, each having a defined area,formed on the surface of a solid support such as, but not limited to,glass, plastic, or synthetic membrane. The density of the discreteregions on a microarray is determined by the total numbers ofimmobilized polynucleotides to be detected on the surface of a singlesolid phase support, such as of at least about 50/cm², at least about100/cm², or at least about 500/cm², up to about 1,000/cm² or higher. Thearrays may contain less than about 500, about 1000, about 1500, about2000, about 2500, or about 3000 immobilized polynucleotides in total. Asused herein, a DNA microarray is an array of oligonucleotide orpolynucleotide probes placed on a chip or other surfaces used tohybridize to amplified or cloned polynucleotides from a sample. Sincethe position of each particular group of probes in the array is known,the identities of a sample polynucleotides can be determined based ontheir binding to a particular position in the microarray.

As an alternative to the use of a microarray, an array of any size on asupport may be used in the practice of the disclosure, including anarrangement of one or more position of a two-dimensional orthree-dimensional arrangement to detect expression of miR-660 or anmRNA.

In some aspects, a label is attached to one or more probes and has oneor more of the following properties: (i) provides a detectable signal;(ii) interacts with a second label to modify the detectable signalprovided by the second label, e.g., FRET (Fluorescent Resonance EnergyTransfer); (iii) stabilizes hybridization, e.g., duplex formation; and(iv) provides a member of a binding complex or affinity set, e.g.,affinity, antibody-antigen, ionic complexes, hapten-ligand (e.g.,biotin-avidin). In still other embodiments, use of labels can beaccomplished using any one of a large number of known techniquesemploying known labels, linkages, linking groups, reagents, reactionconditions, and analysis and purification methods.

miRNAs and mRNAs can be detected by direct or indirect methods. In adirect detection method, one or more miRNAs are detected by a detectablelabel that is linked to a nucleic acid molecule. In such methods, themiRNAs may be labeled prior to binding to the probe. Therefore, bindingis detected by screening for the labeled miRNA that is bound to theprobe. The probe is optionally linked to a bead in the reaction volume.

In certain embodiments, nucleic acids are detected by direct bindingwith a labeled probe, and the probe is subsequently detected. In oneembodiment of the invention, the nucleic acids, such as amplifiedmiRNAs, are detected using FIexMAP Microspheres (Luminex) conjugatedwith probes to capture the desired nucleic acids. Some methods mayinvolve detection with polynucleotide probes modified with fluorescentlabels or branched DNA (bDNA) detection.

In other embodiments, nucleic acids are detected by indirect detectionmethods. For example, a biotinylated probe may be combined with astreptavidin-conjugated dye to detect the bound nucleic acid. Thestreptavidin molecule binds a biotin label on amplified miRNA, and thebound miRNA is detected by detecting the dye molecule attached to thestreptavidin molecule. In one embodiment, the streptavidin-conjugateddye molecule comprises Phycolink® Streptavidin R-Phycoerythrin(PROzyme). Other conjugated dye molecules are known to persons skilledin the art.

Labels include, but are not limited to: light-emitting,light-scattering, and light-absorbing compounds which generate or quencha detectable fluorescent, chemiluminescent, or bioluminescent signal(see, e.g., Kricka, L., Nonisotopic DNA Probe Techniques, AcademicPress, San Diego (1992) and Garman A., Non-Radioactive Labeling,Academic Press (1997).). Fluorescent reporter dyes useful as labelsinclude, but are not limited to, fluoresceins (see, e.g., U.S. Pat. Nos.5,188,934, 6,008,379, and 6,020,481), rhodamines (see, e.g., U.S. Pat.Nos. 5,366,860, 5,847,162, 5,936,087, 6,051,719, and 6,191,278),benzophenoxazines (see, e.g., U.S. Pat. No. 6,140,500), energy-transferfluorescent dyes, comprising pairs of donors and acceptors (see, e.g.,U.S. Pat. Nos. 5,863,727; 5,800,996; and 5,945,526), and cyanines (see,e.g., WO 9745539), lissamine, phycoerythrin, Cy2, Cy3, Cy3.5, Cy5,Cy5.5, Cy7, FluorX (Amersham), Alexa 350, Alexa 430, AMCA, BODIPY630/650, BODIPY 650/665, BODIPY-FL, BODIPY-R6G, BODIPY-TMR, BODIPY-TRX,Cascade Blue, Cy3, Cy5, 6-FAM, Fluorescein Isothiocyanate, HEX, 6-JOE,Oregon Green 488, Oregon Green 500, Oregon Green 514, Pacific Blue, REG,Rhodamine Green, Rhodamine Red, Renographin, ROX, SYPRO, TAMRA,Tetramethylrhodamine, and/or Texas Red, as well as any other fluorescentmoiety capable of generating a detectable signal. Examples offluorescein dyes include, but are not limited to, 6-carboxyfluorescein;2′,4′,1,4,-tetrachlorofluorescein; and2′,4′,5′,7′,1,4-hexachlorofluorescein. In certain aspects, thefluorescent label is selected from SYBR-Green, 6-carboxyfluorescein(“FAM”), TET, ROX, VICTM, and JOE. For example, in certain embodiments,labels are different fluorophores capable of emitting light atdifferent, spectrally-resolvable wavelengths (e.g., 4-differentlycolored fluorophores); certain such labeled probes are known in the artand described above, and in U.S. Pat. No. 6,140,054, incorporated byreference in its entirety. A dual labeled fluorescent probe thatincludes a reporter fluorophore and a quencher fluorophore is used insome embodiments. It will be appreciated that pairs of fluorophores arechosen that have distinct emission spectra so that they can be easilydistinguished.

In still another embodiment, labels are hybridization-stabilizingmoieties which serve to enhance, stabilize, or influence hybridizationof duplexes, e.g., intercalators and intercalating dyes (including, butnot limited to, ethidium bromide and SYBR-Green), minor-groove binders,and cross-linking functional groups (see, e.g., Blackburn et al., eds.“DNA and RNA Structure” in Nucleic Acids in Chemistry and Biology(1996)).

In further aspects, methods relying on hybridization and/or ligation toquantify miRNAs or mRNAs may be used, including oligonucleotide ligation(OLA) methods and methods that allow a distinguishable probe thathybridizes to the target nucleic acid sequence to be separated from anunbound probe. As an example, HARP-like probes, as disclosed in U.S.Publication No. 2006/0078894, incorporated by reference in its entirety,may be used to measure the quantity of miRNAs.

In an additional embodiment of the method, a probe ligation reaction maybe used to quantify miRNAs or mRNAs. In a Multiplex Ligation-dependentProbe Amplification (MLPA) technique (Schouten et al., Nucleic AcidsResearch 30:e57 (2002), incorporated by reference in its entirety),pairs of probes which hybridize immediately adjacent to each other onthe target nucleic acid are ligated to each other only in the presenceof the target nucleic acid. In some aspects, MLPA probes have flankingPCR primer binding sites. MLPA probes can only be amplified if they havebeen ligated, thus allowing for detection and quantification of miRNAbiomarkers.

The methods described herein are useful for application to any lungcancer, for example small cell lung cancer and non-small cell lungcancer, including adenocarcinoma, squamous cell carcinoma and large-celllung cancer.

In one embodiment, reducing MDM2 expression by administration of miR-660inhibits tumor growth. Without wishing to be bound by theory, highexpression level of MDM2 is associated with a poor prognosis. Additionalembodiments of the invention further comprise measuring the expressionlevel of MDM2 in a lung tumor tissue or biological fluid sample of thepatient. In these embodiments, an MDM2 expression level in the lungtumor tissue sample or a biological fluid sample of the patient that isabove an MDM2 expression level in a lung tumor tissue sample from aplurality of lung cancer patients that had a favorable prognosisindicates that the patient has a poor prognosis.

The measurement of expression of proteins such as MDM2 and p53 can be byany means known in the art. In some embodiments, the expression level ofMDM2 or p53 is determined by mRNA expression, as discussed above.

Alternatively, and in further embodiments of the disclosure, geneexpression of proteins such as MDM2 and p53 may be determined byanalysis of expressed protein in a cell sample of interest, for example,by use of one or more binding proteins such as antibodies specific forone or more epitopes of the individual gene products (proteins), orproteolytic fragments thereof, in a cell sample or in a bodily fluid ofa subject. The cell sample may be one enriched from the blood of asubject, such as by use of labeled antibodies against cell surfacemarkers followed by fluorescence activated cell sorting (FACS). Suchantibodies may be labeled to permit their detection after binding to thegene product. Detection methodologies suitable for use in the practiceof the disclosure include, but are not limited to, immunohistochemistryof cell containing samples or tissue, enzyme linked immunosorbent assays(ELISAs) including antibody sandwich assays of cell containing tissuesor blood samples, mass spectroscopy, and immuno-PCR.

One of the effects of the treatment methods described herein is anincrease in p53. Without being bound to any particular mechanism, it isbelieved that the increase in p53 is the cause of the tumor suppressionin this treatment.

Thus, in some embodiments, the invention methods further comprisemeasuring the expression level of p53 in a tumor tissue sample of thepatient. In these embodiments, an absence of p53 in the tumor tissuesample indicates that the patient would not benefit from therapy thatreduces MDM2 expression levels, and where p53 is present, but at anexpression level below a p53 expression level in a lung tumor tissuesample from a plurality of lung cancer patients that had a favorableprognosis, indicates that the patient would benefit from therapy thatreduces MDM2.

The Example below demonstrates that the concentration of miR-660 inbodily fluids of a lung cancer patient is lower than the miR-660 levelis bodily fluids of control subjects that do not have lung cancer.

Thus, a method of diagnosing lung cancer in a patient is provided. Themethod comprises measuring the concentration of miR-660 in a bodilyfluid of the patient. In this method, a miR-660 concentration in thepatient below a miR-660 concentration in a plurality of control subjectsthat do not have lung cancer indicates that the patient has lung cancer.

As discussed above, these embodiments are not narrowly limited to anyparticular bodily fluid. Examples of useful bodily fluids are peripheralblood, serum, plasma, ascites, urine, sputum, saliva, broncheoalveolarlavage fluid, cyst fluid, pleural fluid, peritoneal fluid, lymph, pus,lavage fluids from sinus cavities, bronchopulmonary aspirates, and bonemarrow aspirates.

In some embodiments, the concentration of miR-660 is measured byisolating total RNA from the bodily fluid, reverse transcribing themiR-660 into miR-660 cDNA, and quantifying the miR-660 cDNA usingreal-time PCR.

This method is useful for application to any lung cancer, for examplesmall cell lung cancer and non-small cell lung cancer, includingadenocarcinoma, squamous cell carcinoma and large-cell lung cancer.

In some embodiments, this method further comprises measuring theexpression level of mouse double minute 2 (MDM2) in a lung tumor tissuesample of the patient if the patient has lung cancer. In theseembodiments, an MDM2 expression level in the lung tumor tissue sample ofthe patient that is above an MDM2 expression level in non-canceroustissue indicates that the patient would benefit from therapy thatreduces MDM2 expression levels in the patient's lung tumor tissue.

As previously discussed, the MDM2 expression level may be determined byany means known in the art. In some embodiments, the MDM2 expressionlevel is measured by measuring the MDM2 mRNA level. In otherembodiments, the MDM2 expression level is measured by measuring the MDM2protein level.

The example below also demonstrates that the concentration of miR-660 incancerous lung tissue is lower than in paired normal lung tissue (see,e.g., FIG. 2B). Thus, an additional method of diagnosing lung cancer ina patient is provided. The method comprises measuring the concentrationof mir-660 in (a) tissue suspected of being lung cancer in the patientand (b) normal tissue of the patient, wherein a lower level of miR-660in the suspected tissue than in the normal tissue indicates that thesuspected tissue is lung cancer.

In some embodiments of this method, the non-cancerous tissue is from thepatient. In other embodiments, the non-cancerous tissue is from acontrol subject or a plurality of control subjects.

In various embodiments, this method further comprises measuring theexpression level of p53 in a tumor tissue sample of the patient if thepatient has lung cancer. In these embodiments, an absence of p53 in thetumor tissue sample indicates that the patient would not benefit fromtherapy that reduces MDM2 expression levels, and where p53 is presentbut at an expression level below a p53 expression level in a tissuesample from non-cancerous tissue indicates that the patient wouldbenefit from therapy that reduces MDM2.

In some of these embodiments, the non-cancerous tissue is from thepatient. In some of these embodiments, the normal tissue is obtainedfrom the same specimen as the suspect tissue. In other embodiments, thenon-cancerous tissue is from a control subject or a plurality of controlsubjects.

This method is useful for application to any lung cancer, for examplesmall cell lung cancer and non-small cell lung cancer, includingadenocarcinoma, squamous cell carcinoma and large-cell lung cancer.

The tissue for these embodiments may be obtained by any means, forexample bronchoscopy, needle aspiration, core biopsy, thoracentesis, orthoracotomy. Further, any type of tissue preparation may be used, forexample, fresh frozen tissue of FFPE tissue.

The present invention is further illustrated by reference to thefollowing Examples. However, it is noted that these Examples, like theembodiments described above, are illustrative and are not to beconstrued as restricting the scope of the invention in any way.

EXAMPLES Example. MiR-660 is Down-Regulated in Lung Cancer Patients andits Administration Inhibits Lung Tumorigenesis by Targeting the MDM2-p53Interaction Example Summary

Lung cancer represents the leading cause of cancer-related death indeveloped countries. Despite advances in diagnostic and therapeutictechniques, the 5-year survival rate remains very low. The research fornovel therapies directed to biological targets has modified therapeuticapproaches, but the frequent engagement of resistance mechanisms and thesubstantial costs limit the ability to reduce lung cancer mortality.MicroRNAs (miRNAs) are small non-coding RNAs with regulatory functionsin controlling cancer initiation and progression. In this study we foundthat miR-660 expression is down-regulated in lung tumors compared withadjacent normal tissues and in plasma samples of lung cancer patientswith poor prognosis, suggesting a potential functional role of thismiRNA in lung tumorigenesis. Transient over-expression of miR-660 usingmiRNA mimics reduced migration, invasion, and proliferation propertiesand increased apoptosis in NCI-H460, LT73, and A549 p53 wild-type lungcancer cells. Furthermore, stable over-expression using lentiviralvectors in NCI-H460 and A549 cells inhibited tumor xenograft growth inimmunodeficient mice (95% and 50% reduction compared to control,respectively), whereas the effects of miR-660 over-expression wereabsent in H1299, a lung cancer cell line lacking p53, in both in vitroand in vivo assays. These effects of miR-660 were mediated through mousedouble minute 2 (MDM2), a key regulator of the level and function of p53tumor suppressor protein. MDM2 is thus identified and validated as a newdirect target of miR-660.

MiR-660 thus acts as a tumor suppressor miRNA, and replacement ofmiR-660 expression is a new therapeutic approach for p53 wild-type lungcancer treatment.

Material and Methods

Population study. Tissue and plasma samples were collected fromhigh-risk heavy smoker volunteers aged 50 or older, including current orformer smokers with a minimum pack/year index of 20 enrolled in twoindependent low-dose computed tomography (LDCT) trials performed at theIstituto Nazionale dei Tumori-Istituto Europeo di Oncologia (INT-IEO)and the Multicentric Italian Lung Detection (MILD) trials (Pastorino etal., 2003; Pastorino et al., 2012). Twenty lung cancer patients from theMILD trial were selected for the analysis on tissue samples; 19 lungcancer patients and 27 disease-free individuals grouped in 5 pools fromthe INT-IEO trial were selected for the analysis on plasma samples(Table 1).

TABLE 1 Characteristics of enrolled subjects Trial INT-IEO Trial ILD (n= 18) (n = 20) Gender Male 12 (66.7%) 15 (75.0%) Female  6 (33.3%) 5(25%)  Age (years) 58.4 ± 5.4  61.7 ± 6.6  Smoking habit (Pack-Yearindex) 60.8 ± 23.2   55 ± 19.8 Histotype ADC 14 (77.8%) 14 (70.0%) SCC 3 (16.7%)  5 (25.0%) other 1 (5.5%) 1 (5.0%) Stage Ia-Ib 11 (61.1%) 14(70.0%) II-III-IV  7 (38.9%)  6 (30.0%) Median Follow up (months) 66 26Prognosis Disease free 10 (55.6%) 14 (70.0%) Alive with disease  0 1(5.0%) Dead  8 (44.4%)  5 (25.0%)

MiRNA expression analysis. For plasma samples, total RNA was isolatedfrom 200 μl of plasma using the mirVana™ PARIS kit (LifeTechnologies/Thermo Fisher Scientific) according to the manufacturer'sinstructions and eluted in 50 μl of Elution Buffer. High-throughputanalyses were performed using the Megaplex™ Pools Protocol onmicrofluidic card type A (Life Technologies/Thermo Fisher Scientific) aspreviously described (Boeri et al., 2011).

For tissue samples, total RNA was extracted using Trizol®(Invitrogen/Thermo Fisher Scientific) following manufacturer'sinstructions and quantified using the NanoDrop 2000 (Thermo Scientific).

For cultured cells, total RNA was isolated using mirVana PARIS Kit (LifeTechnologies/Thermo Fisher Scientific) following the manufacturer'sinstructions. Reverse transcription was performed using the TaqMan®microRNA Reverse Transcription Kit according to the manufacturer'sinstruction (Applied Biosystems/Thermo Fisher Scientific). MiRNAexpression was analyzed by the Applied Biosystems 7900 System andnormalized to the small nucleolar RNU6B for tissues and RNU48 for cells.

Cell lines and miRNA transfection. Human lung cancer cell lines, H460,LT73, A549 and H1299, were obtained from the American Type CultureCollection (ATCC). LT73 cells were derived in our laboratory from aprimary lung tumor of a 68-year old Caucasian male with lungadenocarcinoma. Cells were cultured in RPMI 1640 medium supplementedwith 10% heat inactivated fetal bovine serum (FBS) and 1%penicillin-streptomycin (Sigma-Aldrich). Cells were transfected usingmirVana miRNA mimics using Lipofectamine® 2000 (Invitrogen/Thermo FisherScientific) according to the manufacturer's instructions (FIGS. 1A-1C).

Proliferation assay. For proliferation assays, cells were seeded in a12-well plate at 2×10⁵ cells for A549, H1299 and LT73 and 1.5×10⁵ cellsfor H460. Viable cells were counted after 72 and 120 hours by Trypanblue staining. Each experiment was performed in triplicate.

Migration and invasion assay. For migration assays, 10⁵ cells wereplated on the top chamber of FluoroBlok Cell Culture Inserts (BDBiosciences). RPMI plus 10% FBS was added to the bottom chamber andincubated at 37° C. and 5% CO₂. For the invasion assay FluoroBlok CellCulture Inserts were coated with matrigel (BD Biosciences). After 24hours, cells that had migrated to the bottom side of the insert werefixed and stained with DAPI. Migrated cells were counted usingfluorescence microscopy. Migration and invasion data are expressed asthe number of migrated miR-660 over-expressing cells vs. the number ofmigrated control cells.

Apoptosis evaluation. Apoptosis was measured by quantifying thepercentage of Annexin V^(pos)/Propidium Iodide^(neg) cells by flowcytometry. The percentage of apoptotic cells was evaluated 48 hoursafter miRNA transfection using the Annexin V-FITC Kit (Miltenyi Biotec)according to the manufacturer's protocol.

Cell cycle evaluation. Cells were fixed with 70% cold ethanol andstained with propidium iodide (50 μg/ml) for 40 minutes. Cells wereanalyzed by flow cytometry using BD FACS Calibur and Cell Quest software(BD Biosciences).

Western Blot analysis. Proteins were extracted by incubation with RIPAbuffer and quantified by Bradford reagent. Twenty-five micrograms ofprotein were separated on Nupage 4-12% polyacrylamide gels(Invitrogen/Thermo Fisher Scientific) and transferred to polyvinylidenedifluoride membranes (PVDF, GE Healthcare) to be probed with thefollowing antibodies: mouse anti-MDM2 (1:500, Abcam) and rabbitanti-3-actin (1:5000, Sigma). For detection, goat anti-rabbit or goatanti-mouse secondary antibodies conjugated to horseradish peroxidase(1:2000, GE Healthcare) were used. Signal detection was performed viachemiluminescence reaction (ECL, GE Healthcare).

p53 ELISA. P53 protein levels in cancer cells lysates were measuredusing a p53 Human ELISA kit (Abcam) according to manufacturer'sinstructions.

Luciferase assays. To investigate whether MDM2 is a direct target ofmir-660, the 3′ untranslated region (UTR) of MDM2 was purchased fromSwitchgear Genomics. Conserved binding sites in MDM2 3′UTR at position3333-3340 was identified using TargetScan (http://www.targetscan.org).An empty vector was used as control. Furthermore, the predicted targetsite for miR-660 was mutated by direct mutagenesis of thepLightSwitch_MDM2 3′UTR vector, using the PCR-based QuikChange II XLsite-directed mutagenesis kit (Stratagene, La Jolla, Calif.) accordingto the manufacturer's instructions and the following primers: Fw5′-CAAAACCACTTTTACCAAATACAGAGTTAAATTTG-3′ (SEQ ID NO: 9); Rev5′-CAAATTTAACTCTGTATTTGGTAAAAGTGGTTTTG-3′ (SEQ ID NO: 10). The presenceof the mutations was confirmed by sequencing. The different luciferaseconstructs were transfected into HEK293 cells together with miR-660 or ascrambled oligonucleotide sequence (control). Cells were cultured for 48hours and assayed with the Luciferase Reporter Assay System (SwitchgearGenomics).

Generation of stable miR-660 over-expressing cells. To obtain stablemiR-660 over-expressing cells experiments were performed using theSMARTchoice lentiviral vector (Thermo Fisher Scientific). Lung cancercells were seeded at 5×10⁴ in each well of 24-well plates and infectedwith miR-660 or control lentiviral vector at the multiplicity ofinfection (m.o.i) of 10 (10 infectious units for each target cell).After 72 hours, cells were selected with puromycin, and miRNAover-expression was quantified at 10 and 30 days post infection (FIGS.1A-1C).

In vivo assays. Animal studies were performed according to the EthicsCommittee for Animal Experimentation of the Fondazione IRCCS IstitutoNazionale Tumori, according to institutional guidelines previouslydescribed (Workman et al., 2010). All experiments were carried out withfemale CD-1 nude mice or SCID mice, 7-10 weeks old (Charles RiverLaboratories). Mice were maintained in laminar flow rooms, with constanttemperature and humidity and had free access to food and water.

Lung cancer cells, transfected with mimic-660 or control, were harvestedand resuspended in Matrigel/RPMI (1:1). 5×10⁵ cells were injectedsubcutaneously in the flanks of 4 to 6 weeks old female nude mice. Foreach group, 5 mice were used and injections were performed in two flanksof each animal (n=10 tumors/group). Xenograft growth was measured weeklyusing a calliper.

Statistical Analysis. Statistical significance was determined withunpaired or paired t tests. P-values less than 0.05 were consideredstatistically significant.

Results

Diagnostic and prognostic value of miR-660 in plasma and tissue samplesof lung cancer patients. In order to identify miRNAs differentiallyexpressed between 18 lung cancer patients and 27 matched disease-freeindividuals grouped in five pools (Table 1) we first performedhigh-throughput miRNA expression profile of plasma samples collectedduring the INT-IEO LDCT screening trial (Pastorino et al., 2003). Amongthose miRNAs significantly deregulated between patients and controls, wefound that miR-660 was progressively down-modulated in patients withfavorable prognosis (alive) (miR-660 relative expression=0.54±0.35 vs.1.02±0.22, p<0.05) and patients with poor prognosis (dead) (miR-660relative expression=0.21±0.08 vs. 1.02±0.22, p<0.05) (FIG. 2A) comparedto controls.

Twenty paired tumor and normal lung tissues obtained from lung cancerpatients enrolled in the MILD trial (Pastorino et al., 2012) wereselected (Table 1) to determine miR-660 expression in those tissues. Asshown in FIG. 2B, miR-660 was significantly reduced in tumor compared topaired normal lung tissue (miR-660 relative expression=0.38±0.2 vs.1.21±0.85, p<0.05). P53 mutational status was analyzed in the series oflung cancer patients used for tissue microRNA profiling. P53 mutationswere found in 9 out of 20 patients, but the p53 status did not correlate(p=0.37) with mir-660 expression levels.

MiR-660 reduces cancer cell functionality. In order to understand thefunctional role of miR-660 in lung tumorigenesis, a series of in vitroexperiments was performed using commercially available miRNA mimics onfour different lung cancer cell lines (H460, LT73, A549 and H1299).MiR-660 over-expression resulted in a significant decrease of migratory(FIG. 3A) and invasive (FIG. 3B) capacity of the three p53 wild typecancer cell lines, but not of the H1299 lung cancer cell line, whichlacks functional p53. Furthermore, miR-660 led to a reduction in cellproliferation at 72 and 120 hours after mir-660 transfection wasdetected in p53 wild-type cells only (FIG. 4A). To explain the decreasein cell proliferation, apoptosis was evaluated by flow cytometry bymeasuring the AnnexinV^(pos)/PI^(neg) cells in mir-660 transfected celllines and observed a 20-60% increase in the number of apoptotic cellsafter 48 hours compared to cells transfected with mimic control (FIG.4B).

Cell cycle progression was also evaluated after transient transfectionof miR-660. In those studies, there was a significant increase of G0/G1cells indicating a cell cycle arrest (Table 2). Interestingly, theabsence of the effects observed in in vitro experiments in H1299suggested a potential involvement of miR-660 in targeting the p53pathway.

TABLE 2 MiR-660 over-expression induced G0/G1 cell cycle arrest % G0/G1% S % G2/M cells p-value cells cells NCI- Mim-ctr 77.9 ± 1.5 <0.01 12.1± 1.6  7.4 ± 2.0 H460 Mim-660 83.8 ± 1.0 10.8 ± 1.0  3.0 ± 1.3 LT73Mim-ctr 66.1 ± 1.7 0.01 16.7 ± 3.8 15.6 ± 1.6 Mim-660 72.7 ± 1.7 14.1 ±1.0 12.0 ± 1.3 A549 Mim-ctr 56.5 ± 3.2 0.03 19.9 ± 1.3 15.0 ± 3.0Mim-660 62.6 ± 2.3 18.8 ± 1.2 12.9 ± 3.2 H1299 Mim-ctr 81.9 ± 5   0.40 8.2 ± 3.2  6.1 ± 2.5 Mim-660 83.8 ± 3.1  7.5 ± 1.3 5.4 ± 1  All dataare expressed as mean ± SEM. (n = 5, *p < 0.05 vs. mim-ctr)

MDM2 is a direct target of miR-660. Using in silico programs we firstidentified putative miR-660 targets, focusing on those mRNA encoding forproteins that are components of the p53 pathway. The analysis identifiedthe 3′ UTR of MDM2 as a complementary sequence for the binding ofmiR-660 (FIG. 5A). MDM2 is an E3 ligase and its role is thephysiological regulation of p53. To prove that MDM2 is a direct targetof miR-660, a luciferase reporter assay was performed using commercialcustom made 3′ UTR MDM2. There was a strong down-modulation (87%reduction) of the luciferase activity when co-transfected with miR-660(FIG. 5B). Target specificity was verified using a 3′UTR EMPTY vectorand also by site-directed mutagenesis in the putative miR-660 mindingsites, where no change in luciferase activity was observed (FIG. 5B).There was also a significant reduction of MDM2 mRNA 72 hours aftermiR-660 transfection, as measured by Real-Time PCR (% MDM2 mRNAreduction: 60% for NCI-H460; 70% for LT73 and 63% for A549 compared tocontrol) (FIG. 6A), as well as a reduction of MDM2 protein expression,as determined by Western Blot in all tested cell lines (% MDM2 proteinreduction: 39% for NCI-H460; 30% for LT73 and 47% for A549 compared tocontrol) (FIG. 6B). Furthermore, to confirm that the effects of mir-660replacement were p53-dependent, total p53 levels on cell lysates showeda significant increase in p53 protein expression in all cell lines (p53protein increase: 63% for NCI-H460; 37% for LT73 and 67% for A549compared to control) (FIG. 7A).

To demonstrate that the antitumoral activity of mir-660 isp53-dependent, mRNA levels of p21^(WAF1/CIP1), a cyclin-dependent kinaseinhibitor which functions as p53-dependent cell cycle checkpoint, wereanalyzed and a significant increase of p21 levels after mir-660over-expression (2.3 fold increase in NCI-H460; 2.7 in LT73 and 2.4 inA549 compared to control) were observed (FIG. 7B). Accordingly, toconfirm p21^(WAF1/CIP1) mRNA level up-regulation, a western blotanalysis on cell lysates showed a comparable increase of p21^(WAF1/CIP1)protein levels (2.6 fold increase in NCI-H460; 2.5 in LT73 and 1.7 inA549 compared to control) (FIG. 7C).

Interestingly, we observed MDM2 down-modulation was also viable in H1299p53-null cells (% MDM2 reduction: 40%) without stimulation ofp21^(WAF1/CIP1) transcription or protein expression, indicating that thepresence of a functional p53 protein is fundamental for miR-660antitumoral effects through the regulation of MDM2 levels.

MiR-660 stable over-expression has tumor suppressive effects in vitro.In order to obtain a stable mir-660 over-expression in all cell linesused, stable mir-660 transfectants were created using lentiviral vectors(FIGS. 1A-1C). Furthermore, to confirm mir-660 antitumoral activity, invitro assays were performed using stable mir-660 over-expressing cellsand we observed a decrease in migratory (FIG. 8A) and invasive (FIG. 8B)ability of these cells and a reduction in cell proliferation compared tocontrol (FIG. 8C). Stable mir-660 over-expression induced a significantincrease of apoptotic cells measured as the AnnexinV^(pos)/PI^(neg) inNCI-H460 and A549 cells (2.5 fold increase in NCI-H460 and 1.8 in A549compared to control) (FIG. 8D). According to data obtained withtransient transfection, in H1299 cells these effects were totallyabrogated. Interestingly, cell cycle analysis showed a marked increaseof apoptotic cells (subG0) and a strong G0/G1 arrest in NCI-H460 andA549 respectively, whereas no differences were observed in H1299p53-null cells (FIG. 8E and TABLE 3). In all cell lines, stable mir-660over-expression reduced MDM2 protein levels as shown by Western Blotanalysis (48% protein reduction in NCI-H460; 35% in A549 and 45% inH1299 compared to control) (FIG. 8F). Stable mir-660 transfectants ofLT73 cells could not be obtained likely due to the toxicity of GFPreporter gene in this primary established cell line.

TABLE 3 Stable MiR-660 over-expression impaired cell cycle in p53 wtcells % G0/G1 % G2/M cells % S cells cells subG0 NCI- Ctr 61.6 ± 0.424.5 ± 0.2 9.3 ± 1.7 4.5 ± 1.5 460 660 36.4 ± 0.2  7.9 ± 0.2 3.4 ± 0.152.4 ± 0.3  A549 Ctr 50.6 ± 0.3 23.3 ± 1.2 25.9 ± 0.9   0.2 ± 0.06 66072.5 ± 2.9 16.5 ± 1.1 10.6 ± 1.8  0.3 ± 0.2 H1299 Ctr 72.9 ± 1.5 19.1 ±1.8 6.1 ± 0.4 1.9 ± 1.6 660 76.7 ± 2.0 15.6 ± 0.8 7.1 ± 1.2 0.6 ± 0.3All data are expressed as mean ± SEM. (n = 3, *p < 0.05 vs. mim-ctr)

MiR-660 inhibits xenograft tumor growth. Supported by the resultsshowing miR-660 down-regulation in lung cancer patient tissue andplasma, and the antitumoral effects of miR-660 over-expression in invitro assays, the potential role of this miRNA in the inhibition oftumor growth in immunodeficient mice was evaluated.

Subcutaneous injection of miR-660 transiently transfected p53 wild typeNIH-H460 (FIGS. 10A and 11A) and A549 (FIGS. 10B and 111B) cells in nudemice resulted in a slight initial delay in tumor growth. After thisinitial effect (10-15 days for H460 and 30-35 days for A549), tumorsgrew with rates comparable to control transfected cells. On the otherhand, in p53-null H1299 cells (FIGS. 10C and 11C), transfection ofmiR-660 had no effects on xenograft growth.

Twenty days after transient transfection, miR-660 expression levels weresimilar to those of control cells (FIG. 11D), suggesting a correlationbetween miR-660 transient over-expression and the initial delay in tumorgrowth observed in p53 wt cell lines xenografts. Indeed, stabletransfection with miR-660 led to a complete in vivo growth inhibition(95% of reduction compared to control) in H460 cells (p53 wild type)(FIG. 9A). These effects were less pronounced in A549 (50% inhibition)and completely absent in H1299 transfected cells (FIGS. 9B-9C), lackingthe MDM2 negative regulators p14^(arf) (Xie et al., 2005) and p53protein, respectively. These results highlight the central role of theMDM2/p53 pathway in miR-660 mediated effects, including in in vivoxenograft models. Concerning LT73, cells transiently transfected wereinjected in immunodeficient mice and show a delay at 30-35 days comparedto control (data not shown) but stable mir-660 transfectants could notbe obtained likely due to the toxicity of GFP reporter gene in thisprimary established cell line.

DISCUSSION

Despite considerable efforts to improve outcomes for patients withNSCLC, the 5-year overall survival remains around 15% with a minimalimprovement over the last 30 years. Surgical resection and chemotherapyare the most common treatments for lung cancer management, but in thelast decade new targeted therapies directed to specific geneticalterations such as EGFR mutations or ALK translocation has led topositive results in clinical trials (Socinski et al., 2013; Blackhall etal., 2013). However, these tumors account only for the 20% of NSCLCpatients (Gainor and Shaw, 2013) so new research efforts have to bedirected to identify new alternative markers for targeted therapy.

MiRNAs have previously been shown to be involved in the pathogenesis oflung diseases, including lung cancer, by negatively regulating gene andprotein expression by acting as oncogenes or tumor suppressors. Therationale of using miRNA as therapeutics agents in lung cancermanagement is based on two observations: one is that miRNAs play animportant role in lung development (Sozzi et al., 2011) and theirexpression levels are deregulated in lung cancer patients compared tohealthy subjects (Yanaihara et al., 2006). The second observation isthat modulation of miRNA expression, both in vitro and in vivo, canmodify cancer phenotypes (Du et al., 2009; Peng et al., 2013).

The present study demonstrates that miR-660 is down-modulated in plasmaof lung cancer patients and inversely correlated with prognosis.Furthermore, we observed that miR-660 was significantly down-regulatedin lung cancers compared to normal tissues, leading to the finding thatmiR-660 plays a functional role in lung tumorigenesis. By administeringa vector that expresses miR-660, tumor growth inhibition was achievedboth in vitro and in vivo, apparently mediated by miR-660-inducedimpairment of the MDM2/p53 interaction.

The transcription factor p53 is expressed at low concentrations innormal cells, where it plays an important role in cell cycle regulation(Leonard et al., 1995). Under physiological conditions, p53 levels aresuppressed by the activity of MDM2. Disruption of the p53-MDM2interaction is the pivotal event for p53 activation, leading to p53stabilization and its biological functions, such as cell growth control,apoptosis, and modulation of cell migration (Roger et al., 2006;Vousden, 2000).

The over-expression of miR-660 also decreased the migratory and invasivecapacity of lung cancer cells. This effect was absent in H1299, ap53-null cell line, suggesting a potential role of p53 in controllingtumor migration and invasion. P53 regulates cell migration through themodulation of cell morphology. In particular, p53 prevents filopodiaformation through p38 MAPK activation (Gadea et al., 2004), andderegulates the actin cytoskeleton organization. Another potentialmechanism of p53 inhibition of tumor cell motility is the inhibition ofspreading and polarization of the migrating cells (Gadea et al., 2004).These studies also show that miR-660 overexpression leads to a block ofproliferation in the G0/G1 checkpoint, and induction of apoptosis in ap53 dependent manner. These effects were achieved by in vitroreplacement of miR-660 in p53 wild type NIH-H460 and A549 cells, whereasin H1299 p53-null cells no effects were appreciable on cell cycle or onapoptosis even if a decrease of MDM2 expression levels is observed.Similar results were obtained in in vivo experiments where a significantinhibition of tumor xenograft growth was obtained with miR-660 stabletransfection in NIH-H460 cells and not with miR-660 stable transfectionin p53-null H1299 cells. The hypothesis that miR-660 inhibition of tumorgrowth is mediated by its effects on MDM2 expression and consequently onits impact on p53 pathway is further confirmed by the mild effect ontumor xenograft growth of miR-660 stable transfection in A549, a cellline with an impairment in the p53 pathway due to the loss of p14arf, aninhibitor of MDM2 resulting in hyper-activation of this protein (Wang etal., 2005).

P53 tumor suppressor activity is frequently inactivated by mutations inNSCLC patients (Herbst et al. (2008). N Engl J Med 359, pp. 1367-1380;Yokota and Kohno, 2004) or by MDM2 which eliminates wild-type p53(Freedman et al., 1999). MDM2 was found to be amplified in a portion ofhuman cancers (Higashiyama et al., 1997) and in tumors that retainwild-type p53, inhibitors of MDM2 may have therapeutic value by inducingp53-dependent cytostasis or apoptosis (Bottger et al., 1997).

Upon mir-660 replacement, both in transient or in stable transfections,a tumor growth inhibition effect was shown, in vitro and in vivo, likelymediated by mir-660-induced impairment of the MDM2/p53 interaction. Thetranscription factor p53 is expressed at low concentration in normalcells and it plays an important role in cell cycle regulation. Inphysiological condition, p53 levels are suppressed by the activity ofMDM2. Disruption of the p53-MDM2 interaction is the pivotal event forp53 activation, leading to p53 stabilization and its biologicalfunctions, such as cell growth control, apoptosis, and modulation ofcell migration.

MiR-660 overexpression led to arrest of proliferation in G0/G1checkpoint and induction of apoptosis in a p53-dependent manner. Indeed,these effects were achieved by in vitro replacement of mir-660 in p53wild type NCI-H460 and A549 cells whereas in H1299 p53-null cells noeffects were appreciable on cell cycle or on apoptosis even if adecrease of MDM2 expression levels was detected. It was also shown thatmir-660 induced p53 stabilization and increased its transcriptionalactivity resulting in an up-regulation of its target gene,p21^(WAF1/CIP1) which regulates cell cycle through inhibition ofcyclin-dependent kinases required for progression from G1 to S phase andit is also involved in the apoptotic process.

Similar results were obtained in in vivo experiments where a significantinhibition of tumor xenograft growth was obtained with mir-660 stabletransfection of NCI-H460 and A549 cells and not of p53-null H1299 cells.

Several studies indicate that p53 tumor suppressor activity isfrequently inactivated in NSCLC patients by mutations (53% of all lungcancer) or by interaction with MDM2 which eliminates wild-type p53. MDM2amplification occurs in 7% of human tumors with varying degrees ofamplification between tumor types such as liposarcoma (50-90%),osteosarcomas (16%), esophageal carcinomas (13%), and NSCLC (6%).Notably, MDM2 amplification and p53 mutations are essentially mutuallyexclusive and, in the past few years, small-molecule antagonists ofp53-MDM2 interaction as nutlins or MDM2 inhibitors have been developed.

These observations suggest that reconstitution of p53-dependent pathwaysin tumor cells is an effective therapeutic strategy and restoration ofp53 activity using mir-660 represents an attractive approach for lungcancer therapy. The principal advantage of using miRNAs as therapeuticagent is that they could target several genes of redundant pathways andthus potentially able to achieve a broad silencing of pro-tumoralpathways. A very preliminary bioinformatic analysis revealed thatmir-660 potentially targets several transcription factors, proteases andother regulators of cell growth and survival. Interestingly, we showedthat relatively small changes in the expression of miRNA and its targetgene could induce relevant phenotypic alterations of lung cancer cells,both in vitro and in vivo.

These results provide evidence that mir-660 behaves as a tumorsuppressor miRNA in lung cancer and that mir-660 replacement couldrepresent a potential nontoxic successful therapy for a large subset oflung cancer patients where p53 locus is not genetically altered bymutation or deletion.

In view of the above, it will be seen that several objectives of theinvention are achieved and other advantages attained.

As various changes could be made in the above methods and compositionswithout departing from the scope of the invention, it is intended thatall matter contained in the above description and shown in theaccompanying drawings shall be interpreted as illustrative and not in alimiting sense.

All references cited in this specification are hereby incorporated byreference. The discussion of the references herein is intended merely tosummarize the assertions made by the authors and no admission is madethat any reference constitutes prior art. Applicants reserve the rightto challenge the accuracy and pertinence of the cited references.

The following publications are incorporated by reference herein in theirentireties for all purposes.

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1. A method of treating lung cancer in a patient in need thereof, themethod comprising administering to the patient a composition comprisinga therapeutically effective amount of a compound that reduces theexpression level of E3 ubiquitin-protein ligase MDM2.
 2. A method oftreating lung cancer in a patient in need thereof, the method comprisingadministering to the patient a composition comprising a therapeuticallyeffective amount of a miR-660, or a functional variant thereof to treatat least one symptom of lung cancer, wherein the patient in need oftreatment (i) expresses miR-660 in a lung tissue sample or biologicalfluid sample at a level lower than a control level derived from asubject or plurality of subjects that do not have lung cancer, or ascompared to a control level derived from a lung cancer patient orplurality thereof, that have been given a favorable prognosis; (ii)expresses MDM2 at a higher level in a lung tissue sample or biologicalfluid sample as compared to a control level derived from a subject orplurality of subjects that do not have lung cancer, or as compared to acontrol level derived from a lung cancer patient or plurality thereofthat have been given a favorable prognosis; and/or (iii) expresses p53in a lung tissue sample or a biological fluid sample below a controllevel derived from a lung tumor tissue sample (or plurality thereof) ora biological fluid sample (or plurality thereof) obtained from a patientthat has a favorable lung cancer prognosis; or a control level derivedfrom a healthy subject.
 3. The method of claim 1, wherein the compoundreduces protein expression of the E3 ubiquitin-protein ligase MDM2. 4.The method of claim 1, wherein the compound reduces expression of themRNA encoding the E3 ubiquitin-protein ligase MDM2.
 5. The method ofclaim 1, wherein the compound is an antisense RNA, a small interferingRNA (siRNA), short hairpin RNA (shRNA) or a microRNA (miR). 6.(canceled)
 7. The method of claim 1, wherein the compound is a miR andwherein the miR is miR-660 or a functional variant thereof.
 8. Themethod of claim 7, wherein miR-660 has the sequence of SEQ ID NO: 2 orSEQ ID NO: 3, or a functional variant thereof.
 9. The method of claim 8,wherein the functional variant is at least 80% identical or at least 90%identical in sequence to SEQ ID NO: 2 or SEQ ID NO:
 3. 10. The method ofclaim 7, wherein the miR-660 or functional variant thereof comprises oneor more modified nucleotides. 11-14. (canceled)
 15. The method of claim7, wherein the miR-660 or functional variant thereof comprises thesequence ACCCAUU (SEQ ID NO: 4) or ACCCATT (SEQ ID NO: 5). 16-19.(canceled)
 20. The method of claim 1, wherein a lung tumor tissue sampleor a biological fluid sample from the patient in need of treatmentexpresses p53.
 21. The method of claim 20, wherein the lung tumor sampleor the biological fluid sample from the patient in need of treatmentexpresses p53 below a control level derived from a lung tumor tissuesample, or a plurality thereof, or a biological fluid sample, orplurality thereof, obtained from a patient that has a favorable lungcancer prognosis; or a control level derived from a lung tissue sampleor biological fluid sample obtained from a healthy subject or aplurality of healthy subjects.
 22. The method of claim 1, wherein thepatient in need of treatment expresses miR-660 in a lung tissue sampleor biological fluid sample at a level lower than a control level derivedfrom a subject or plurality of subjects that do not have lung cancer, oras compared to a control level derived from a lung tumor sample orbiological fluid sample obtained from a cancer patient or pluralitythereof, that have been given a favorable prognosis;
 23. The method ofclaim 1, wherein the patient in need of treatment expresses MDM2 at ahigher level in a lung tissue sample or biological fluid sample ascompared to a control level derived from a lung tissue sample orbiological fluid obtained from a subject or plurality of subjects thatdo not have lung cancer, or as compared to a control level derived froma lung tissue sample or biological fluid sample obtained from a lungcancer patient or plurality thereof that have been given a favorableprognosis.
 24. The method of claim 1, wherein a miR-660 level in aplasma sample from the patient in need of treatment is below a miR-660level in a plasma sample from a healthy subject or the average miR-660plasma level in a plurality of healthy subjects.
 25. The method of claim1, wherein a lung tumor tissue sample from the patient in need oftreatment expresses MDM2 protein.
 26. The method of claim 1, wherein alung tumor tissue sample from the patient in need of treatment expressesMDM2 mRNA.
 27. The method of claim 25, wherein the MDM2 expression levelin the lung tumor tissue is greater than an MDM2 level in a noncancerouslung tissue sample from the patient in need of treatment or a healthysubject.
 28. The method of claim 1, wherein the patient in need oftreatment is identified by a method comprising: (a) determining theexpression ratio of a miRNA pair in a biological sample from thepatient; (b) comparing the expression ratio from step (a) with a cut-offvalue determined from the average ratio of a plurality of correspondingmiRNA pairs from a plurality of control samples; (c) assigning apositive score for the expression ratio of the miRNA pair in step (a) ifthe ratio exceeds the cut-off value in step (b); (d) repeating steps (a)through (c) for additional miRNA pairs until either (1) at least ninemiRNA pair expression ratios are assigned a positive score, or (2) afterthe comparison of the expression ratios of 27 miRNA pairs less than ninemiRNA pair expression ratios are assigned a positive score, wherein themiRNA pairs comprise 106a/140-5p, 106a/142-3p, 126/140-5p, 126/142-3p,133a/142-3p, 140-5p/17, 142-3p/148a, 142-3p/15b, 142-3p/17, 142-3p/21,142-3p/221, 142-3p/30b, or 320/660, or the inverse ratios thereof; and(e) categorizing the presence of a pulmonary tumor as (i) positive if atleast nine of the miRNA pair expression ratios are assigned a positivescore, or (ii) negative if less than nine miRNA pair expression ratiosare assigned a positive score.
 29. The method of claim 28, wherein themiRNA pairs further comprise 106a/660, 106a/92a, 126/660, 140-5p/197,140-5p/28-3p, 142-3p/145, 142-3p/197, 142-3p/28-3p, 17/660, 17/92a,197/660, 197/92a, 19b/660, or 28-3p/660, or the inverse ratios thereof.